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PROPOSAL 1—RE-ELECTION OF KEVIN LEE TO THE BOARD OF DIRECTORS

Dr. Kevin Lee, Ph.D., MBA, is currently a member of the Board and has been nominated for re-election as a director. If re-elected, he will hold office until the 2027 annual general meeting of the shareholders, when he must retire by rotation and offer himself for re-election, or until his earlier death, resignation or removal. If re-elected, Dr. Lee will continue to serve as a member of our Board. Dr. Lee has agreed to serve if re-elected, and we have no reason to believe that he will be unable to serve.

Dr. Lee has served as our Chief Executive Officer and a member of our Board since September 2015. From April 2012 to September 2015, Dr. Lee serviced as Senior Vice President and Chief Scientific Officer of the Rare Disease Research Unit at Pfizer Inc. Prior to that, Dr. Lee worked at GlaxoSmithKline plc, where in addition to leading the formation of multiple strategic commercial and academic partnerships, he led epigenetics research and was responsible for the creation of the EpiNova Discovery Performance Unit. Before joining GlaxoSmithKline, Dr. Lee was a lecturer at Warwick University Medical School and founded Cambridge Biotechnology Ltd, which specialized in developing small molecule and peptide therapeutics for inflammation and metabolic diseases before its trade sale to Biovitrum in 2005 and Neurosolutions (now Oncosil Medical Ltd ASX). Dr. Lee received a BPharm from Nottingham University and a Ph.D. in pharmacology from Cambridge University. Dr. Lee has an MBA from Warwick Business School and currently serves as a non-executive director at Alchemab Ltd., a position he has held since June 2021, and as a non-executive director at Macomics Ltd, a position he has held since July 2023. Dr. Lee also served as a non-executive director of Nodthera from 2018 to 2023. We believe that Dr. Lee is qualified to serve on our Board based on his extensive leadership, executive, managerial, business and pharmaceutical and biotechnology company experience, along with his years of industry experience in the development and commercialization of pharmaceutical products.

Vote Required

The affirmative vote of holders representing a simple majority of the total voting rights of shareholders present in person or by proxy who (being entitled to vote) vote on the matter will be required to re-elect Dr. Lee to the Board of Directors as a Class II director.

Our Recommendation

THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE RE-ELECTION

OF KEVIN LEE TO THE BOARD OF DIRECTORS AS A CLASS II DIRECTOR

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PROPOSAL 2—RE-ELECTION OF JOSE-CARLOS GUTIERREZ-RAMOS TO THE BOARD OF DIRECTORS

Dr. Jose-Carlos Gutierrez-Ramos, Ph.D., is currently a member of our Board and has been nominated for re-election as a director. If re-elected, he will hold office until the 2027 annual general meeting of the shareholders, when he must retire by rotation and offer himself for re-election, or until his earlier death, resignation or removal. Dr. Gutierrez-Ramos has agreed to serve if re-elected, and we have no reason to believe that he will be unable to serve.

Dr. Gutierrez-Ramos has served as a director since March 2021. Since January 2021, Dr. Gutierrez-Ramos has served as the Chief Science Officer at Danaher Corporation, a publicly traded science and technology company. Prior to that, Dr. Gutierrez-Ramos was the Global Head of Global Drug Discovery at AbbVie, Inc., a publicly traded biopharmaceutical company, from February 2020 to January 2021. From June 2018 to February 2020, he was the Chief Executive Officer and President of Repertoire Immune Medicine Inc., a biotechnology company. From 2015 to May 2018, he served as Chief Executive Officer and president of Synlogic, Inc., a biotechnology company. Earlier in his career, Dr. Gutierrez-Ramos held positions at Pfizer Inc., GlaxoSmithKline plc, and Millennium Pharmaceuticals, Inc. Dr. Gutierrez-Ramos also served on the board of directors of Momenta Pharmaceuticals (acquired by Johnson & Johnson) from March 2016 to October 2020. Dr. Gutierrez-Ramos received a B.S. from Universidad Complutense de Madrid and his Ph.D. in immunochemistry from the Universidad Autonoma de Madrid. We believe that Dr. Gutierrez-Ramos is qualified to serve on our Board based on his executive experience at pharmaceutical and biotechnology companies, as well as his prior experience with our company based on his service on our Scientific Advisory Board from 2017 to 2019.

Vote Required

The affirmative vote of holders representing a simple majority of the total voting rights of shareholders present in person or by proxy who (being entitled to vote) vote on the matter will be required to re-elect Dr. Gutierrez-Ramos to the Board of Directors as a Class II director.

Our Recommendation

THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE RE-ELECTION

OF JOSE-CARLOS GUTIERREZ-RAMOS TO THE BOARD OF DIRECTORS AS A CLASS II DIRECTOR

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PROPOSAL 3—ADVISORY VOTE ON EXECUTIVE COMPENSATION

At the 2022 Annual General Meeting, the shareholders indicated their preference that the Company solicit a non-binding advisory vote on the compensation of the named executive officers, commonly referred to as a “say-on-pay vote,” every year. The Board has adopted a policy that is consistent with that preference. In accordance with that policy, this year, the Company is again asking the shareholders which is the third anniversary of the AGM, and until his successor is elected and has been qualified, or until his earlier death, resignation or removal.

In connection with proposals 1 and 2, we set forth the biographical information for the nominees to our Board. For biographical information for the other directors, see the section of this proxy statement titled “Board of Directors and Corporate Governance.”

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PROPOSAL 4—ADVISORY VOTE ON THE FREQUENCY OF SOLICITATION OF ADVISORY SHAREHOLDER APPROVAL OF EXECUTIVE COMPENSATION

The Dodd-Frank Act and Section 14A of the Exchange Act also enable our shareholders, at least once every six years, to indicate their preference regarding how frequently we should solicit a non-binding advisory vote on the compensation of our named executive officers as disclosed in the Company’s proxy statement. Accordingly, we are asking shareholders to indicate whether they would prefer an advisory vote every year, every other year or every three years. Alternatively, shareholders may abstain from casting a vote.

After considering the benefits and consequences of each alternative, the Board recommends that the advisory vote on the compensation of our named executive officers be submitted to shareholders each year.

The Board believes that an annual advisory vote on the compensation of our named executive officers is the most appropriate policy for us at this time. While our executive compensation program is designed to promote the creation of shareholder value over the long term, the Board recognizes that executive compensation disclosures are made annually, and holding an annual advisory vote on the compensation of our named executive officers provides us with more direct and immediate feedback on our executive compensation program, policies and disclosures. However, shareholders should note that because a proposed annual advisory vote would occur well after the beginning of the compensation year, and because the different elements of our executive compensation programs are designed to operate in an integrated manner and to complement one another, in many cases it may not be appropriate or feasible to change our compensation plans and arrangements for our executive officers in consideration of any single year’s advisory vote by the time of the following year’s annual meeting of shareholders. We believe, however, that an annual advisory vote on the compensation of our named executive officers is consistent with our practice of seeking input and engaging in dialogue with our shareholders on corporate governance matters.

Vote Required

While the Board believes that its recommendation is appropriate at this time, the shareholders are not voting to approve or disapprove that recommendation, but are instead asked to indicate their preferences, on an advisory basis, as to whether the non-binding advisory vote on the approval of our executive officer compensation practices should be held every year, every other year or every three years. You may cast your vote on your preferred voting frequency by choosing the option of “1 year,” “2 years,” “3 years,” or abstain from voting when you vote. The option that receives the highest number of votes cast by shareholders will be the frequency for the advisory vote on executive compensation that has been selected by shareholders.

The Board and the Compensation Committee value the opinions of the shareholders in this matter and, to the extent there is any significant vote in favor of one frequency over the other options, even if less than a majority, the Board will consider the shareholders’ concerns and evaluate any appropriate next steps. The Board may decide, however, because this vote is advisory and, therefore, not binding on the Board or the Company, that it is in the best interests of the shareholders that the Company hold an advisory vote on executive compensation more or less frequently than the option preferred by the shareholders. The vote will not be construed to create or imply any change or addition to the fiduciary duties of the Company or the Board.

Our Recommendation

THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR “1 YEAR”

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Pre-Approval Policies and Procedures

The Audit Committee has adopted a policy and procedures for the pre-approval of audit, review and attest services and permitted non-audit services rendered by PwC. The policy generally permits the Audit Committee to pre-approve, on an annual basis, specified services in the defined categories of audit services, audit-related services, tax services and other permitted non-audit services. Pre-approval may also be given as part of the Audit Committee’s approval of the scope of the engagement of the auditor or on an individual, explicit, case-by-case basis before the auditor is engaged to provide each service.

The Audit Committee has determined that the rendering of certain services other than audit services by PwC are compatible with maintaining the accounting firm’s independence.

The Audit Committee has delegated to its chair the authority, from time to time, to pre-approve non-audit services not prohibited by law to be performed by our independent auditors and associated fees, provided that the estimated fees for such permitted non-audit services do not exceed specified thresholds and provided that the chair shall report any decisions to pre-approve such non-audit services and fees to our full Audit Committee at its next regular meeting.

Vote Required

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The affirmative vote of holders representing a simple of a majority of the total voting rights of shareholders present in person or by proxy who (being entitled to vote) vote on the matter will be required to ratify the appointment of PricewaterhouseCoopers LLP as our U.S. independent registered public accounting firm, to re-appoint PricewaterhouseCoopers LLP as our U.K. statutory auditors and to authorize our Audit Committee to determine our U.K. statutory auditors’ remuneration for the year ending December 31, 2022.2024.

THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE:

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PROPOSAL 9—7—RESOLUTION TO RECEIVE AND ADOPT OUR 20212023 U.K. ANNUAL REPORT

In accordance with the Companies Act, our Board is required to present our 20212023 U.K. Annual Report, which includes the audited portion of the directors’ annualremuneration report, on remuneration, to the shareholders at the AGM. We will provide our shareholders with an opportunity to raise questions in relation to the 20212023 U.K. Annual Report at the AGM. In accordance with best practice, we are proposing an ordinary resolution to receive and adopt the 20212023 U.K. Annual Report.

The 20212023 U.K. Annual Report may be found in the AGMInvestor section of our website at https://investors.bicycletherapeutics.com.

Vote Required

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The affirmative vote of holders representing a simple of a majority of the total voting rights of shareholders present in person or by proxy who (being entitled to vote) vote on the matter will be required to receive and adopt the 20212023 U.K. Annual Report.

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THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE RESOLUTION

TO RECEIVE AND ADOPT OUR 20212023 U.K. ANNUAL REPORT

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PROPOSAL 10—8—APPROVAL OF OUR U.K. STATUTORY DIRECTORS’ ANNUALREMUNERATION REPORT ON REMUNERATION

The Companies Act requires that our directors’ remuneration report, as set forth asin Annex A to this proxy statement, and on pages 28 to 55 of the 2021 U.K. Annual Report, be subject to an annual advisory vote. Accordingly, we are asking shareholders to approve, on an advisory basis, the directors’ remuneration report.

Our Board considersbelieves that appropriate remuneration of directors plays a vital part in helping to achieve our overall objectives. We encourage shareholders to read the directors’ remuneration report. Our Board and the Compensation Committee believe that the policies and procedures as articulated in the directors’ remuneration report are effective and that as a result of these policies and procedures we have and will continue to have high-quality directors. Our U.K. statutory auditors, PwC, have audited those parts of the directors’ remuneration report that are required to be audited. Our Board has approved and signed the directors’ remuneration report in accordance with English law.

For the avoidance of doubt, the directors’ remuneration policy was approved by shareholders in a binding vote at the AGM on June 13, 2023 and took effect from the date of approval and will continue to apply for a maximum period of three years (or until a revised policy is approved by shareholders). The directors’ remuneration policy is unchanged this year, and as such is not subject to a shareholder vote.

Vote Required

The affirmative vote of holders representing a simple majority of the total voting rights of shareholders present in person or by proxy who (being entitled to vote) vote on the matter will be required to pass this resolution.

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This vote is advisory and non-binding and the directors’ entitlement to receive remuneration is not conditional on it. Payments made or promised to directors will not have to be repaid, reduced or withheld in the event that the resolution is not passed. Although non-binding, our Board and Compensation Committee will review and consider the voting results when making future decisions regarding our director remuneration program. Following the AGM, and as required under English law, the directors’ annualremuneration report on remuneration will be delivered to the U.K. Registrar of Companies.

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THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR APPROVAL OF OUR U.K. STATUTORYTHE

DIRECTORS’ ANNUALREMUNERATION REPORT ON REMUNERATION SET FORTH IN ANNEX A

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BACKGROUND TO PROPOSALS 9 AND 10

Introduction

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As a matter of English law, directors of an English public company must have specific authority from shareholders to allot shares in the company or to grant rights to subscribe for or to convert any security into shares in the company (other than pursuant to employee equity plans). In addition, when the directors of an English public company allot equity securities (being ordinary shares or rights to subscribe for, or to convert any securities into, ordinary shares) for cash, the company must first offer those equity securities on the same or more favorable terms to existing shareholders of the company on a pro rata basis (commonly referred to as the statutory pre-emption right) unless this statutory pre-emption right is disapplied, or opted-out of, by approval of the shareholders. In this proxy statement, we refer to the share allotment authority and pre-emption disapplication collectively as the “share issuance authorities.”

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At the 2021 annual general meeting of shareholders held on June 28, 2021 (“2021 AGM”), our shareholders authorized our directors to allot shares or to grant rights to subscribe for or to convert any securities into shares in the Company up to a maximum aggregate nominal value of £250,000 (equal to 25 million shares with a nominal value of £0.01 each) and disapplied the statutory pre-emption right in respect of such allotments, in each case for a period of up to five years.

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The share issuance authorities granted at the 2021 AGM have, since the 2021 AGM, kept us on an equal footing with our peer companies who are incorporated and listed in the United States. However, following the issuance of shares in our follow-on offerings in October 2021 and July 2023, under our at-the-market (“ATM”) program through 2023, and through grants of options and restricted share units to non-employees, the remaining unutilized portion of the share issuance authorities from the 2021 AGM is an aggregate nominal value of less than £80,000 and we are therefore seeking approval from our shareholders of a renewal of our share issuance authorities at this AGM.

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Proposals 9 and 10, which we refer to as our Share Issuance Proposals, ask our shareholders to approve, for a period of up to five years, the allotment of shares and grant of rights to subscribe for, or convert any security into, shares in the Company of up to a maximum aggregate nominal value of £1,000,000 (equal to 100 million shares with a nominal value of £0.01 each) on a non-pre-emptive basis. We are and will continue to be subject to all of the shareholder approval and other requirements that arise from our ADSs being listed exclusively on the Nasdaq Global Select Market and our being considered a U.S. domestic reporting company under SEC rules, and our Board will also continue to focus on and satisfy its duties to our shareholders with respect to share issuances.

Many of our peer companies are listed and incorporated in the United States and are not subject to similar share issuance restrictions. We are asking you to approve our Share Issuance Proposals to allow us to continue to execute on our business and growth strategy in a timely manner.

Rationale for Seeking Renewal of Current Share Issuance Authorities

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Ability to execute on our business and growth strategy without competitive disadvantage

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The renewal of our share issuance authorities is fundamental to the way we intend to advance our business and increase shareholder value. Our strategy to maximize the value of our novel technology and pipeline requires us to devote significant financial resources to research and development activities, including preclinical studies and clinical trials, which to date have principally been funded through equity offerings and our ATM program. Not having the flexibility to undertake equity offerings when and in such manner as our Board considers in the best interests of shareholders could put us at a distinct disadvantage vis-à-vis many of our peer companies that are listed and incorporated in the United States and are not subject to similar share issuance restrictions.

Likewise, the requirement to first offer shares that we propose to issue for cash to all of our existing shareholders in time-consuming pro-rata rights offerings would considerably reduce the speed at which we could complete capital-raising activities undertaken in furtherance of our growth strategy, increase our costs and decrease the

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certainty of completion of any such transaction, all of which would put us at a distinct disadvantage vis-à-vis many of our peers.

We do not believe that limitations derived from U.K. market practice should apply to Bicycle

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While not required by English law, it is market practice for companies whose shares are listed on the premium segment of the London Stock Exchange to seek authorities at their annual general meeting each year which comply with U.K. institutional investor guidelines applicable to such companies. Companies with shares listed on the standard segment of the London Stock Exchange or on the London Stock Exchange’s AIM market are encouraged to follow the guidelines. These guidelines require the authority to allot shares to be sought annually and to be limited to up to two-thirds of the existing issued share capital, with any amount in excess of one-third of existing issued shares to be used for a fully pre-emptive offering only. In addition, the issue of shares for cash on a non-pre-emptive basis is limited to (i) no more than 10% of the existing issued share capital in any one year, (ii) an additional up to 10% that can be used only in connection with an acquisition or specified capital investment and (iii) an additional 2% of issued share capital, plus an additional 2% to be used only in connection with an acquisition or specified capital investment, which may be used only for a follow-on offer to retail investors and existing shareholders after a placing of equity securities. These guidelines are set out in the Investment Association’s Share Capital Management Guidelines and the Pre-Emption Group’s Statement of Principles, respectively.

While these limitations in size and duration on the share issuance authorities are part of the corporate governance framework applicable to companies whose share capital is listed on the London Stock Exchange (regardless of whether such companies are incorporated in the United Kingdom or elsewhere), our ordinary shares are not, and never have been, listed on the London Stock Exchange, and we are not subject to London Stock Exchange share listing rules or governed by the corporate governance standards applicable to companies whose share capital is listed on the London Stock Exchange.

As an English company, we are committed to complying with English law. We are legally required to seek shareholder approval to renew our share issuance authorities because we are incorporated in England and Wales. However, the U.S. capital markets are the sole capital markets for our ordinary shares and our securities are listed solely on the Nasdaq Global Select Market. As such, we believe that our shareholders expect us to, and we are committed to, follow customary U.S. capital markets practices, U.S. corporate governance standards, the rules and regulations of the SEC and the Nasdaq rules and listing standards. We also believe that applying the standards and market practices of a market where our securities are not listed is inappropriate and is simply not in the best interests of our company or our shareholders, especially in circumstances where we are committed to complying with the governance rules and practices of the actual capital market for our ordinary shares—the Nasdaq Global Select Market—which provides its own separate restrictions on share issuances for the protection of shareholders.

Further, we believe that these U.K. market limitations would leave us disadvantaged as compared with our U.S. incorporated and exchange-listed peers. Companies that are incorporated and listed in the United States are not generally required to—and do not—seek shareholder approval to renew their authority to allot and issue shares, and the dis-application of the statutory pre-emption right is not otherwise required for many companies with which we compete. In this regard, companies who are incorporated and publicly traded in the United States generally do not grant all existing shareholders pre-emptive rights on new issuances of shares.

To be clear, shareholder approval of our Share Issuance Proposals would not mean that we would have no limits on future share issuances. To the contrary, we are considered to be a U.S. domestic reporting company under SEC rules and are subject to the same governance and share issuance requirements as all other U.S.-incorporated companies listed on Nasdaq. For example, Nasdaq rules generally require shareholder approval prior to our issuing shares in connection with acquisitions, other than in public offerings for cash, when the number of shares to be issued is or will be equal to or in excess of 20% of the number of our ordinary shares outstanding before the issuance. With limited exceptions, we must also seek shareholder approval of our equity compensation plans, including material revisions of such plans.

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We understand that certain proxy advisory firms apply their U.K. voting guidelines in formulating their voting recommendations on share issuance authorities proposals for U.S.-listed U.K. incorporated companies, meaning that they have applied or otherwise taken into account the market practice for companies whose share capital is listed on the London Stock Exchange in formulating their voting recommendations on share issuance authorities proposals for U.K. incorporated companies, even if their shares are not listed on the London Stock Exchange (or any other U.K. exchange). For all of the reasons stated above, we respectfully disagree with this approach.

We also understand that some U.K. incorporated companies that are listed solely on U.S. stock exchanges have followed the market practice for companies whose share capital is listed on the London Stock Exchange with respect to their own share issuance authorities proposals. However, those companies may have business and growth strategies that differ from ours or may have different approaches for creating shareholder value.

In summary, because the Share Issuance Proposals are fully compliant with English corporate law, consistent with U.S. capital markets practice and governance standards, and, if approved, will keep us on an equal footing with our peer companies who are incorporated and listed in the United States, we believe it is necessary to seek the broad authority to issue new shares on a non-pre-emptive basis as is contemplated by the Share Issuance Proposals.

Summary

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The Share Issuance Proposals, if approved, will maintain the status quo and provide our Board continued flexibility to issue shares, subject to the shareholder approval and other requirements of Nasdaq and the SEC. The renewal of the share issuance authorities, as proposed:

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For the above reasons, our Board strongly recommends that you vote “FOR” each of the Share Issuance Proposals.

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PROPOSAL 9—AUTHORIZATION OF ALLOTMENT OF SHARES

The directors of an English public limited company must have specific authority from shareholders to allot shares in the company or to grant rights to subscribe for or to convert any security into shares in the company.

At the 2021 AGM, our shareholders authorized our directors to allot shares or to grant rights to subscribe for or convert any security into shares in the Company up to a maximum aggregate nominal value of £250,000 (equal to 25 million shares with a nominal value of £0.01 each), for a period of up to five years. Following the issuance of shares in follow-on offerings, our ATM program and through the grant of options and restricted share units to non-employees, the remaining unutilized share issuance authorities will only allow us to allot shares or grant rights to subscribe for or to convert any security into shares in the Company of a maximum aggregate nominal value of less than £80,000 (equal to 8 million shares with a nominal value of £0.01 each).

We are asking for your approval to renew the directors’ authority to allot shares for an additional five-year period to expire in May 2029 in respect of shares with an aggregate nominal value of £1,000,000 (equal to 100 million shares with a nominal value of £0.01 each). Your approval of this Proposal 9 will provide our Board with continued flexibility to issue shares or grant rights to subscribe for or to convert any security into shares in the Company up to such maximum aggregate nominal value, subject to the shareholder approval and other requirements of Nasdaq and the SEC. The renewed authority would apply to the issuance of shares, grant of rights to subscribe for or to convert any security into shares in the Company, employee and director equity awards (save to the extent that they are granted under “employee share schemes” and therefore exempt from this requirement) and other securities convertible into or exercisable or exchangeable for our shares.

Renewal of this authority would not exempt us from applicable Nasdaq requirements to obtain shareholder approval prior to certain share issuances or to comply with applicable SEC disclosure and other regulations, and our Board will continue to focus on and satisfy its fiduciary duties to our shareholders with respect to share issuances.

If shareholders do not approve this Proposal 9, the remaining unutilized authorization granted at the 2021 AGM will continue to apply until June 2026 or until such time as it has been fully utilized. However, given that the remaining unutilized portion of the share issuance authorities is now less than an aggregate nominal value of £80,000 (equal to 8 million shares with a nominal value of £0.01 each), our Board may be constrained in its ability to fund the development of our business through further equity offerings in the medium to longer term.

Please refer to background discussion of Proposals 9 and 10 beginning on page 17 of this proxy statement for additional information regarding this proposal.

Vote Required

The affirmative vote of holders representing a simple majority of the total voting rights of shareholders present in person or by proxy who (being entitled to vote) vote on the matter will be required to pass this resolution.

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THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE

AUTHORIZATION OF ALLOTMENT OF SHARES

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PROPOSAL 10—DISAPPLICATION OF PRE-EMPTION RIGHTS

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When the directors of an English public company allot equity securities (being ordinary shares or rights to subscribe for, or to convert any securities into, ordinary shares) for cash, the company must first offer those equity securities on the same or more favorable terms to existing shareholders of the company on a pro rata basis (commonly referred to as the statutory pre-emption right) unless this statutory pre-emption right is disapplied, or opted-out of, by approval of the shareholders.

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At the 2021 AGM, our shareholders disapplied the statutory pre-emption right in respect of allotments of shares or grant of rights to subscribe for or to convert any security into shares in the Company by our directors of up to a maximum aggregate nominal value of £250,000 for a period of up to five years. Following the issuance of shares in follow-on offerings, under our ATM program and through the grant of options and restricted share units to non-employees, the remaining unutilized portion of this disapplication of pre-emption rights is an aggregate nominal value of less than £80,000 (equal to 8 million shares with a nominal value of £0.01 each).

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We are asking for your approval to renew the pre-emption disapplication for an additional five-year period to expire in May 2029 in respect of shares with an aggregate nominal value of £1,000,000 (equal to 100 million shares with a nominal value of £0.01 each). Your approval of this Proposal 10 will provide our Board with continued flexibility to issue shares for cash or grant rights to subscribe for, or convert any security into, shares for cash on a non-pre-emptive basis up to such maximum aggregate nominal value.

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Renewal of this authority would not exempt us from applicable Nasdaq requirements to obtain shareholder approval prior to certain share issuances or to comply with applicable SEC disclosure and other regulations, and our Board will continue to focus on and satisfy its fiduciary duties to our shareholders with respect to share issuances.

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If shareholders do not approve Proposal 9 or this Proposal 10, the remaining unutilized disapplication of pre-emption rights granted at the 2021 AGM will continue to apply until June 2026 or until it has been fully utilized. Shares issued for cash in excess of such number or after such time would have to first be offered to our existing shareholders pro rata to their existing shareholdings before those shares could be issued to any new shareholders. If Proposal 9 is approved by shareholders but this Proposal 10 is not, we would have no remaining disapplication of pre-emption rights as the disapplication of pre-emption rights granted at the 2021 AGM related to the allotment authority granted at the 2021 AGM which would have been replaced by the allotment authority granted in Proposal 9. This limitation on our ability to issue shares for cash could put us at a distinct disadvantage vis-à-vis many of our peers who are not subject to such requirements, and would increase our costs and otherwise might make it difficult for us to complete equity capital financings that our Board considers to be in the best interests of our shareholders. Please note that the requirement to offer shares to pre-existing shareholders does not apply where such shares are issued for non-cash consideration or pursuant to employee share schemes.

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Please refer to background discussion of Proposals 9 and 10 beginning on page 17 of this proxy statement for additional information regarding this proposal.

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Voting Required

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The approval of this Proposal 10 is conditional on the approval of Proposal 9 because English law requires that a pre-emption disapplication be given in respect of a particular authorization (general or specific) to allot shares. Proposal 10 will therefore not be passed unless Proposal 9 is also approved, notwithstanding that shareholders may have voted to approve Proposal 10. As required under English law, Proposal 10 is a special resolution that requires the affirmative vote of at least 75% of the votes cast in person or by proxy at the AGM in order to be approved.

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THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE

DISAPPLICATION OF PRE-EMPTION RIGHTS

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PROPOSAL 11—ADOPTION OF NEW ARTICLES OF ASSOCIATION

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In July 2023, we issued 4,705,882 non-voting ordinary shares, nominal value £0.01 per share, to certain investors as part of an underwritten public offering. Following the offering, we have two classes of ordinary shares: voting ordinary shares and non-voting ordinary shares. The Board of Directors approved the terms of issue of the non-voting ordinary shares which sets out the rights of the holders of non-voting ordinary shares (the “Terms of Issue”).

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Further, our current articles of association provide that (i) two shareholders present in person or by proxy and entitled to attend and vote on the business to be transacted shall constitute a quorum at general meetings and (ii) in the event of an adjourned general meeting or class meeting at least one shareholder, or shareholder of the relevant class, present in person or by proxy shall be a quorum. Nasdaq Listing Rule 5620(c), however, defines a quorum as no less than 33 1/3 percent of the outstanding shares of a company’s voting stock. We are therefore taking this opportunity to amend the definition of quorum in our current articles of association so that it conforms to Nasdaq Listing Rule 5620(c).

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Our shareholders are therefore asked to approve the adoption of new articles of association in order to incorporate the terms of the non-voting ordinary shares as set out in the Terms of Issue into our articles of association and to amend the definition of quorum for purposes of shareholder actions at general meetings and meetings of holders of classes of shares to conform with Nasdaq Listing Rule 5620(c).

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Therefore, it is proposed that Articles 2, 4, 10, 12.3, 52 and 53 of our current articles of association be amended in the new articles of association to incorporate the terms of the non-voting ordinary shares as set out in the Terms of Issue and to amend the definition of quorum (collectively, the “Proposed Amendments”):

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2Interpretation

2.1In these Articles, the following words and expressions shall have the meanings set out below:

“Beneficial Ownership Limitation”means 9.99% of any class of securities of the Company registered under the Exchange Act, which percentage may be increased or decreased on a holder-by-holder basis by a holder of Non-Voting Ordinary Shares to such other percentage as such holder may designate in writing (with any increase to be effective upon at least sixty one days’ notice) to the Company, provided, however, that: (i) any such increase shall not exceed 19.9% of any class of securities of the Company registered under the Exchange Act; and (ii) any such increase or decrease shall only be applicable to such holder in relation to such securities. For the purpose of calculating the Beneficial Ownership Limitation, a holder may rely on the number of outstanding shares of the subject class as stated in the most recent of the following:

Upon the written request of a holder (which may be by email with confirmation), the Company shall, within five business days thereof, confirm in writing to such holder (which may be via email) the number of shares then outstanding

“business day” means a day other than Saturday, Sunday or other day on which commercial banks in New York and/or London are authorised or required by law to remain closed

“Exchange Act” means U.S. Securities Exchange Act of 1934 and the rules and regulations promulgated thereunder

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“Non-Voting Ordinary Shares” means the Company’s non-voting ordinary shares with a nominal value of £0.01 each

“Non-Voting Ordinary Shares Re-Designation Notice” has the meaning given to it in Article 10.7

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4Capital

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The capital of the Company is divided into an unlimited number of ordinary shares of £0.01 each (“Ordinary Shares”) and an unlimited number of Non-Voting Ordinary Shares conferring on the holders the rights and being subject to the restrictions set out in Article 10.

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10Shareholder Rights

10.1       The Ordinary Shares shall rank pari passu as a single class. The Non-Voting Ordinary Shares shall rank pari passu as a single class and pari passu with the Ordinary Shares save as set out in Article 10.6 below.

10.2                        In the event of the liquidation, dissolution or winding up of the Company, the assets of the Company available for distribution to members shall be distributed amongst all holders of the Ordinary Shares and Non-Voting Ordinary Shares (if any) in proportion to the number of shares held irrespective of the amount paid or credited as paid on any share.

10.5       A holder of Ordinary Shares is entitled to receive notice of any general meeting of the Company (and notice of any separate class meeting of the holders of Ordinary Shares) and a copy of every report, accounts, circular or other document sent out by the Company to members. A holder of Non-Voting

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Ordinary Shares is entitled to receive notice of any separate class meeting of the holders of Non-Voting Ordinary Shares and a copy of every report, accounts, circular or other document (not being a notice of a general meeting of the shareholders save in relation to a variation of class rights of the Non-Voting Ordinary Shares, or any accompanying proxy statement or circular in respect of such general meeting) sent out by the Company to members.

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re-designated as Ordinary Shares by the Board, or a duly authorised committee or representative thereof.

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52.Quorum at General Meeting

No business shall be transacted at any general meeting unless a quorum is present. If a quorum is not present, a chairman of the meeting can still be chosen and this will not be treated as part of the business of the meeting. A quorum shall be present if both:

(a) two qualifying persons are present at a meeting unless each is a qualifying person only because (i) he is authorised to act as the representative of a corporation in relation to the meeting, and they are representatives of the same corporation, or (ii) he is appointed as proxy of a member in relation to the meeting, and they are proxies of the same member; and

(b)those qualifying persons present together hold (or are the representative or proxy of members in relation to the meeting holding) at least one-third (33 1/3 percent) of the number of the

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issued shares (excluding any shares held as treasury shares) entitled to vote on the business to be transacted.

For the purposes of this Article 52, (A) a “qualifying person” is an individual who is a member, a person authorised to act as the representative of a member (being a corporation) in relation to the meeting or a person appointed as proxy of a member in relation to the meeting and (B) where a qualifying person is present as proxy of a member in relation to the meeting, only the shares in respect of which the proxy is authorised to exercise voting rights will be treated as held for the purposes of determining whether a quorum is present.

53.Procedure if Quorum Not Present

If a quorum is not present within 15 minutes (or such longer interval as the chairman in his absolute discretion thinks fit) from the time appointed for holding a general meeting, or if a quorum ceases to be present during a meeting, the meeting shall be dissolved if convened on the requisition of members. In any other case, the meeting shall stand adjourned to another day, (not being less than ten clear days after the date of the original meeting), and at such time and place or places, with such means of attendance and participation (including partly, but not wholly, by means of electronic facility or facilities), as the chairman (or, in default, the Board) may determine. If at such adjourned meeting a quorum is not present within 15 minutes from the time appointed for holding the meeting, the meeting shall be dissolved.

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In addition, we are proposing to amend Article 59.6 of our current articles of association to correct a typographical error.

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This description of the Proposed Amendments is qualified in its entirety by reference to, and should be read in conjunction with, the full text of the articles of association as they are proposed to be adopted included as Annex B to this proxy statement, in which we have shown the proposed amendments colored in red, with deletions indicated by strikeouts and additions indicated by underlining.

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Proposal 11 will be required to be passed as a special resolution. If our shareholders approve Proposal 11, the new articles of association would become effective from the conclusion of the AGM.

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Voting Required

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As required under English law, Proposal 11 is a special resolution that requires the affirmative vote of at least 75% of the votes cast in person or by proxy at the AGM in order to be approved.

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THE BOARD OF DIRECTORS RECOMMENDS A VOTE FOR THE

ADOPTION OF NEW ARTICLES OF ASSOCIATION

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BOARD OF DIRECTORS AND CORPORATE GOVERNANCE

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Board of Directors

Our nominees for re-election as directors at the AGM are bothall currently serving as members of our Board. Information about each such nominee is set forth in the proposals 1 and 2 and is incorporated into this section by reference. Set forth below is a list of our directors and their ages as of the date of this proxy statement.

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Biographical information for those directors who are not standing for re-election at the AGM and who will remain seated following the AGM, including each such individual’s principal occupation, business experience and education, and an explanation of the qualifications, skills and experiences that we believe are relevant to such individual’s service on our Board, are set forth below. Mr. Legault’sDr. Lee’s and Mr. Kender’sDr. Gutierrez-Ramos’ biographies are set forth above in Proposals 1 and 2, respectively.

Kevin Lee Ph.D.,Pierre Legault, MBA, CA, CPA has served as our Chief Executive OfficerChairman and a member of our Board since September 2015. From April 2012 to September 2015, Dr. LeeMarch 2019. Mr. Legault has also served as Senior Vice Presidenta consultant to us since March 2019. Mr. Legault has served as Chairman and a member of the boards of directors of Egle Therapeutics since March 2022, Sitryx Therapeutics Limited since March 2021, Amolyt Pharma SA since December 2020 and Artios Pharma Limited since February 2018. Mr. Legault has served on the board of directors of Syndax Pharmaceuticals since January 2017. Mr. Legault also previously served as Chairman of Poxel SA from March 2016 to March 2023, and as a member of the boards of directors at Urovant Sciences Ltd, Clementia Pharmaceuticals, Forest Laboratories, Tobira Therapeutics, NPS Pharmaceuticals, Regado Biosciences, Armo Biosciences, Iroko Pharmaceuticals, Cyclacel Pharmaceuticals and Eckard Pharmacy. Mr. Legault also previously served as Chairman and Chief ScientificExecutive Officer of NephroGenex, as Chief Executive Officer of Prosidion Ltd., a subsidiary of Astellas Pharma Inc., as Chief Financial Officer and Treasurer of OSI Pharmaceuticals, Inc., as Chief Executive Officer of Eckerd Pharmacy and as Chief Administrative Officer of the Rare Disease Research UnitRite Aid Corporation. Mr. Legault held various global roles such as President, Chief Executive Officer and Chief Financial Officer at Pfizer Inc., a pharmaceutical company. From November 2004 to April 2012, Dr. Lee worked at GlaxoSmithKline plc, where in addition to leading the formation of multiple strategic commercial and academic partnerships, he led epigenetics research and was responsible for the creationlegacy companies of the EpiNova Discovery Performance Unit. Before joining GlaxoSmithKline, Dr. Lee wasSanofi-Aventis group. Mr. Legault earned a lecturer at Warwick University Medical School and founded Cambridge Biotechnology Ltd, which specializedB.B.A. in developing small molecule and peptide therapeutics for inflammation and metabolic diseases before its trade sale to BiovitrumBusiness & International Finance from HEC Montreal, an MBA in 2005 and Neurosolutions (now Oncosil Medical Ltd ASX). Dr. Lee received a BPharmMarketing from NottinghamMcGill University and a Ph.D. in pharmacology from Cambridge University. Dr. Lee has an MBA from Warwickholds C.A. and C.P.A. diplomas. He also studied at Harvard Business School and currently serves as a non-executive director for Nodthera Ltd, a position he has held since October 2018, and as a non-executive director at Alchemab Ltd., a position he has held since May 2021.in their Graduate Executive MBA program. We believe that Dr. LeeMr. Legault is qualified to serve on our Board based on his extensive leadership, executive, managerial, businessexperience leading and pharmaceutical and biotechnology company experience, along with his yearsmanaging a number of industry experience in the development and commercialization of pharmaceutical products.biopharmaceutical companies.

Janice Bourque, MBAhas served as a member of our Board since July 2019. Ms. Bourque is a Managing Director in Hercules Capital'sCapital’s life sciences group and has more than 2530 years of life science experience and a focus on emerging growth stage companies. Previously, Ms. Bourque has consulted for Commons Capital, served as Senior Vice President and Group Head, Life Sciences at Comerica Bank and was President and Chief Executive Officer of the Massachusetts Biotechnology Council. Ms. Bourque currently serves on the board of directors of The Village Bank. Ms. Bourque also previously served on the board of directors of Poxel SA and the Village Bank.from January 2016 to March 2023. Ms. Bourque has also served on the board of directors of the MIT Koch Institute for Integrative Cancer Research. She holds a B.S. in veterinary science and an MBA in finance and accounting from the University of New Hampshire. We believe that Ms. Bourque is qualified to serve on our Board based on her extensive experience as a senior executive and board member in the life sciences sector.

Veronica Jordan, Ph.D. has served as a member of our Board since October 2019. Dr. Jordan has been a corporate director for more than 15 years, with extensive experience in the biopharmaceutical industry, and has been an advisor to companies developing novel healthcare products. Since 2007, Dr. Jordan has served as an independent

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consultant to healthcare companies and contract research organizations and as Managing Director of Golden Seeds, an angel investor network.organizations. She was previously CEO and President of Medelle Corporation, a private medical device company, and held various executive roles at PAREXEL International during her 14 years on the company's

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Board Diversity

The Board diversity matrix, below, provides the diversity statistics for our Board of Directors. Our previous year’s disclosure can be found in our definitive proxy statement filed with the Securities and Exchange Commission on April 28, 2023.

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Role of the Board in Risk Oversight

Our Board believes that risk management is an important part of establishing, updating and executing on our business strategy. Our Board, as a whole and at the committee level, has oversight responsibility relating to risks that could affect our corporate strategy, business objectives, compliance, operations, financial condition and performance. Our Board focuses its oversight on the most significant risks facing our company and on its processes to identify, prioritize, assess, manage and mitigate those risks. Our Board and its committees receive regular reports from members of our senior management on areas of material risk to us, including strategic, operational, financial, legal and regulatory risks. While our Board has an oversight role, management is principally tasked with direct responsibility for management and assessment of risks and the implementation of processes and controls to mitigate their effects on our company.

Our Audit Committee, as part of its responsibilities, oversees the management of financial risks, including accounting matters, liquidity and credit risks, corporate tax positions, insurance coverage, and cash investment strategy and results. Our Audit Committee is also responsible for overseeing the management of risks relating to the performance of our internal audit function, if required, and our independent registered public accounting firm, as well as our systems of internal controls and disclosure controls and procedures and risks related to data privacy and cybersecurity. Additionally, pursuant to its charter, the Audit Committee may retain, as necessary, subject matter experts and advisers to assist in its oversight of risk management within our company. Our Compensation Committee is responsible for overseeing the management of risks relating to our executive compensation and overall compensation and benefit strategies, plans, arrangements, practices and policies. Our Nominating and Corporate Governance Committee oversees the management of risks associated with our overall compliance and corporate governance practices and the independence and composition of our Board. It is the responsibility of the committee chairs to report findings regarding material risk exposures to the Board as quickly as possible. While the Board and its committees oversee risk management strategy, management is responsible for implementing and supervising day-to-day risk management processes and reporting to the Board and its committees on such matters.

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Committees of our Board of Directors

Our Board has established a standing Audit Committee, Compensation Committee and Nominating and Corporate Governance Committee. The following table provides membership and meeting information for each committee for the year ended December 31, 2021:2023:

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AUDIT COMMITTEE REPORT

The material in this report is not “soliciting material,” is not deemed filed with the SEC and is not to be incorporated by reference in any filing of the Company under the Securities Act of 1933, as amended (the “Securities Act”), or the Securities Exchange Act of 1934, as amended (the “Exchange Act”), whether made before or after the date hereof and irrespective of any general incorporation language in any such filing.

The Audit Committee has reviewed and discussed the audited financial statements for the fiscal year ended December 31, 20212023 with management of the Company. The Audit Committee has discussed with the U.S. independent registered public accounting firm the matters required to be discussed by the applicable requirements of the Public Company Accounting Oversight Board (“PCAOB”) and the SEC. The Audit Committee has also received the written disclosures and the letter from the independent registered public accounting firm required by applicable requirements of the PCAOB regarding the independent accountants’ communications with the Audit Committee concerning independence, and has discussed with the U.S. independent registered public accounting firm the accounting firm’s independence. Based on the foregoing, the Audit Committee recommended to the Board that the audited financial statements be included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2021.2023.

The Audit Committee of the Board of Directors

Richard Kender, Chair

Janice Bourque

Veronica Jordan

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Compensation Committee

Our Compensation Committee is currently composed of Janice Bourque, Veronica Jordan and Richard Kender, with Dr. Jordan serving as chair of the committee. The Compensation Committee held eight meetings during 2021.

The Compensation Committee’s responsibilities include:

Nominating and Corporate Governance Committee

Our Nominating and Corporate Governance Committee is composed of Janice Bourque and Jose-Carlos Gutierrez-Ramos, with Ms. Bourque serving as chair of the committee. The Nominating and Corporate Governance Committee held five meetings during 2021.

The Nominating and Corporate Governance Committee’s responsibilities include:

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Director Nomination Process

Our Nominating and Corporate Governance Committee is responsible for identifying individuals qualified to serve as directors, consistent with criteria approved by our Board, and recommending such persons to be nominated for election as directors, except where we are legally required by contract, law or otherwise to provide third parties with the right to nominate.

The Board, upon the recommendation of the Nominating and Corporate Governance Committee periodically determines the characteristics, skills and experience required to be a director and develops criteria to be considered in selecting nominees for director. The Board believes that candidates for director should have certain minimum qualifications, including: experience at a strategic or policymaking level in a business, government, non-profit or academic organization of high standing; proven achievement and competence in the nominee’s field and the ability to exercise sound business judgment; high standards of personal and professional ethics and integrity; having sufficient time to devote to the affairs of our company; and a demonstrated history of actively contributing at board meetings if the nominee serves or has previously served on other boards. However, the Board retains the right to modify these qualifications from time to time. Candidates for director nominees are also reviewed in the context of the current composition of the Board, the operating requirements of our company and the long-term interests of shareholders. In conducting this assessment, the Board and the Nominating and Corporate Governance Committee typically consider diversity, age, skills and such other factors as it deems appropriate, given the current needs of the Board and our company, to maintain a balance of knowledge, experience and capability. The Board also determines whether the nominee is independent for Nasdaq purposes, which determination is based upon applicable Nasdaq listing standards, applicable SEC rules and regulations and the advice of counsel, if necessary.

In the case of incumbent directors whose terms of office are set to expire, the Nominating and Corporate Governance Committee reviews these directors’ overall service to our company during their terms, including the number of meetings attended, level of participation, quality of performance and any other relationships and transactions that might impair the directors’ independence. The Committee will take into account the results of the Board’s self-evaluation, conducted annually on a group and individual basis.

Generally, our Nominating and Corporate Governance Committee identifies candidates for director nominees in consultation with management, using search firms or other advisors, through the recommendations submitted by shareholders or through such other methods as the Nominating and Corporate Governance Committee deems to be helpful to identify candidates. The Nominating and Corporate Governance Committee conducts any appropriate and necessary inquiries into the backgrounds and qualifications of possible candidates after considering the function and needs of the Board. The Nominating and Corporate Governance Committee meets to discuss and consider the candidates’ qualifications and then selects a nominee for recommendation to the Board by majority vote. The Nominating and Corporate Governance Committee may gather information about the candidates through interviews, questionnaires, background checks or any other means that the Nominating and Corporate Governance Committee deems to be appropriate in the evaluation process. We have no formal policy regarding board diversity.

Shareholder Recommendations and Nominees

It is the policy of our Board that the Nominating and Corporate Governance Committee consider both recommendations and nominations for candidates to the Board from shareholders so long as such recommendations and nominations comply with our Articles of Association and applicable laws, including the rules and regulations of the SEC. Shareholders may recommend director nominees for consideration by sending a written request to Bicycle Therapeutics plc, Blocks A & B, Portway Building, 900 Babraham Research Campus, Babraham,Granta Park, Great Abington, Cambridge, CB22 3AT,CB21 6GS, United

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Kingdom, Attn: Jim Sutcliffe, Company Secretary. The shareholder must also provide the shareholder’s name and address of record, a representation that the shareholder is a record holder of our securities (or, if not a record holder, evidence of ownership in accordance with Rule 14a-8(b)(2) of the Exchange Act), the nominee’s name, age, business and residential addresses, educational background, current principal occupation or employment, and principal occupation or employment for the

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SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

The following table and related footnotes set forth information with respect to the beneficial ownership of our ordinary shares, as of April 7, 2022,March 29, 2024, by:

Beneficial ownership is determined in accordance with the rules and regulations of the SEC. Under these rules, beneficial ownership includes any shares as to which a person has sole or shared voting power or investment power. In computing the number of ordinary shares beneficially owned by a person and the percentage ownership of that person, ordinary shares subject to options, or other rights held by such person that are currently exercisable or will become exercisable within 60 days of April 7, 2022March 29, 2024 are considered outstanding. These ordinary shares, however, are not included in the computation of the percentage ownership of any other person. Applicable percentage ownership is based on 29,646,43837,926,715 ordinary shares outstanding as of April 7, 2022.March 29, 2024.

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Unless otherwise indicated, the address for each of the shareholders listed in the table below is c/o Bicycle Therapeutics plc, Blocks A & B, Portway Building, 900 Babraham Research Campus, Babraham,Granta Park, Great Abington, Cambridge, CB22 3AT,CB21 6GS, United Kingdom.