<Page>
EXHIBIT 10.13
AXCELIS TECHNOLOGIES, INC.
EMPLOYEE STOCK PURCHASE PLAN
ADOPTED BY THE BOARD OF DIRECTORS AND THE SOLE STOCKHOLDER ON JUNE 9, 2000, AND
EFFECTIVE ON JULY 10, 2000
AS AMENDED BY THE BOARD OF DIRECTORS ON
JANUARY 27, 2005 (STOCKHOLDER APPROVAL NOT REQUIRED)
TO BE EFFECTIVE JULY 1, 2005
1. PURPOSE.
The purpose of this Plan is to provide an opportunity for Employees of
Axcelis Technologies, Inc. (the "Corporation") and its Designated Subsidiaries,
to purchase Common Stock of the Corporation and thereby to have an additional
incentive to contribute to the prosperity of the Corporation. It is the
intention of the Corporation that the Plan qualifies as an "Employee Stock
Purchase Plan" under Section 423 of the Internal Revenue Code of 1986, as
amended.
2. DEFINITIONS.
(a) "BOARD" shall mean the Board of Directors of the Corporation.
(b) "CODE" shall mean the Internal Revenue Code of 1986, as amended.
Any reference to a section of the Code herein shall be a reference to any
successor or amended section of the Code.
(c) "COMMITTEE" shall mean the committee appointed by the Board in
accordance with Section 14 of the Plan.
(d) "COMMON STOCK" shall mean the Common Stock of the Corporation, or
any stock into which such Common Stock may be converted.
(e) "COMPENSATION" shall mean base pay, including pay under any system
which measures earnings by quantity and quality of production, variable pay,
including without limitation, bonuses and incentive payments (but excluding
sign-on bonuses and bonuses paid under the Axcelis Team Incentive Plan, and any
successors to such plans and any other similar management bonuses or incentive
payments), shift premium and overtime pay, but excluding severance pay in a
single lump sum and not as salary continuation, pay in lieu of vacation,
cost-of-living allowance, retainers, fees, and any other special remuneration,
with any modifications determined by the Committee. The Committee shall have the
authority to determine and approve all forms of pay to be
<Page>
included in the definition of Compensation and may change the definition on a
prospective basis.
(f) "CORPORATION" shall mean Axcelis Technologies, Inc., a Delaware
corporation.
(g) "DESIGNATED SUBSIDIARY" shall mean a Subsidiary that has been
designated by the Committee as eligible to participate in the Plan with respect
to its Employees.
(h) "EMPLOYEE" shall mean an individual classified as an employee
(within the meaning of Code Section 3401(c) and the regulations thereunder) by
the Corporation or a Designated Subsidiary on the Corporation's or such
Designated Subsidiary's payroll records during the relevant participation
period. Employees shall not include individuals classified as independent
contractors.
(i) "ENTRY DATE" shall mean the first Trading Day of an Offering
Period.
(j) "FAIR MARKET VALUE" shall be the closing sales price for the
Common Stock (or the closing bid, if no sales were reported) as quoted on the
NASDAQ National Market, or other principal securities market on which the Common
Stock is traded, on the date of determination if that date is a Trading Day, or
if the date of determination is not a Trading Day, the last market Trading Day
prior to the date of determination, as reported in THE WALL STREET JOURNAL or
such other source as the Committee deems reliable.
(k) "OFFERING PERIOD" shall mean the period of six (6)months
commencing on the first Trading Day on or about July 1 of every year and
terminating on the last Trading Day in the period ending six (6) months later.
Subsequent Offering Periods, if any, shall run consecutively after the
termination of the preceding Offering Period. The duration and timing of
Offering Periods may be changed or modified by the Committee.
(l) "PARTICIPANT" shall mean a participant in the Plan as described in
Section 5 of the Plan.
(m) "PLAN" shall mean the Axcelis Technologies, Inc. Employee Stock
Purchase Plan.
(n) "PURCHASE DATE" shall mean the last Trading Day of each Offering
Period.
(o) "PURCHASE PRICE" shall mean 85% of the Fair Market Value of a
share of Common Stock on the Entry Date or on the Purchase Date, whichever is
lower; provided
2
<Page>
however, that the Purchase Price may be adjusted by the Committee pursuant to
Section 7.4.
(q) "SHAREHOLDER" shall mean a record holder of shares entitled to
vote shares of Common Stock under the Corporation's by-laws.
(r) "SUBSIDIARY" shall mean any corporation (other than the
Corporation) in an unbroken chain of corporations beginning with the
Corporation, as described in Code Section 424(f).
(s) "TRADING DAY" shall mean a day on which U.S. national stock
exchanges and the NASDAQ System are open for trading.
3. ELIGIBILITY.
3.1 Any Employee regularly employed on a full-time or part-time basis
by the Corporation or by any Designated Subsidiary on an Entry Date shall be
eligible to participate in the Plan with respect to the Offering Period
commencing on such Entry Date, provided that the Committee may establish
administrative rules requiring that employment commence some minimum period
(e.g., one pay period) prior to an Entry Date to be eligible to participate with
respect to the Offering Period beginning on that Entry Date.
3.2 The Committee may also determine that a designated group of highly
compensated Employees are ineligible to participate in the Plan so long as the
excluded category fits within the definition of "highly compensated employee" in
Code Section 414(q). No Employee may participate in the Plan if immediately
after an option is granted the Employee owns or is considered to own (within the
meaning of Code Section 424(d)), shares of stock, including stock which the
Employee may purchase by conversion of convertible securities or under
outstanding options granted by the Corporation, possessing five percent (5%) or
more of the total combined voting power or value of all classes of stock of the
Corporation or of any of its Subsidiaries.
3.3 All Employees who participate in the Plan shall have the same
rights and privileges under the Plan except for differences which may be
mandated by local law and which are consistent with Code Section 423(b)(5);
provided, however, that any affiliate of the Corporation whose Employees are not
granted options under this Plan may adopt a separate "sub-plan" in accordance
with the provisions of Section 15 which is not designed to qualify under Code
section 423 and the Employees participating thereunder need not have the same
rights and privileges as Employees participating in the Code section 423 Plan.
The Board may impose restrictions on eligibility and participation of Employees
who are officers and directors to facilitate compliance with federal or state
securities laws or foreign laws.
3
<Page>
4. OFFERING PERIODS.
The Plan shall be implemented by consecutive Offering Periods with a new
Offering Period commencing on the first Trading Day on or after the date six (6)
months from the first date of the immediately preceding Offering Period, or on
such other date as the Committee shall determine, and continuing thereafter for
six (6) months or until terminated pursuant to Section 13 hereof. Unless
otherwise determined by the Committee, the Plan will operate with successive six
(6) month Offering Periods commencing at July 1 and January 1. The Committee
shall have the power to change the duration of future Offering Periods, without
Shareholder approval, and without regard to the expectations of any
Participants.
4.1 The Committee shall have the authority to change the duration of
Offering Periods (including the commencement dates thereof) with respect to
future offerings without Shareholder approval if such change is announced at
least five (5) days prior to the scheduled beginning of the first Offering
Period to be affected thereafter.
5. PARTICIPATION.
5.1 An Employee who is eligible to participate in the Plan in
accordance with Section 3 may become a Participant by completing and submitting,
on a date prescribed by the Committee prior to an applicable Entry Date (unless
a later date is set by the Committee), a completed payroll deduction
authorization and Plan enrollment form provided by the Corporation or by
following an electronic or other enrollment process as prescribed by the
Committee. An eligible Employee may authorize payroll deductions at the rate of
any whole percentage of the Employee's Compensation, not to exceed ten percent
(10%) of the Employee's Compensation. As determined by the Committee, payroll
deductions may begin at a date after the effective date of the Plan. All payroll
deductions may be held by the Corporation and commingled with its other
corporate funds where administratively appropriate. No interest shall be paid or
credited to the Participant with respect to such payroll deductions. The
Corporation shall maintain a separate bookkeeping account for each Participant
under the Plan and the amount of each Participant's payroll deductions shall be
credited to such account. A Participant may not make any additional payments
into such account.
5.2 Under procedures established by the Committee, a Participant may
withdraw from the Plan during an Offering Period, by completing and filing a new
payroll deduction authorization and Plan enrollment form with the Corporation or
by following electronic or other procedures prescribed by the Committee, prior
to a date set by the Committee that precedes the Purchase Date. If a Participant
withdraws from the Plan during an Offering Period, his or her accumulated
payroll deductions will be
4
<Page>
refunded to the Participant without interest. The Committee may establish rules
limiting the frequency with which Participants may withdraw and re-enroll in the
Plan and may impose a waiting period on Participants wishing to re-enroll
following withdrawal.
5.3 A Participant may change his or her rate of contribution through
payroll deductions during the periods specified by the Committee by filing a new
payroll deduction authorization and Plan enrollment form or by following
electronic or other procedures prescribed by the Committee. If a Participant has
not followed such procedures to change the rate of contribution, the rate of
contribution shall continue at the originally elected rate throughout the
Offering Period and future Offering Periods. In accordance with Section
423(b)(8) of the Code, the Committee may reduce a Participant's payroll
deductions to zero percent (0%) at any time during an Offering Period.
6. TERMINATION OF EMPLOYMENT.
In the event any Participant terminates employment with the Corporation
or any of its Designated Subsidiaries for any reason (including death) prior to
the expiration of a Offering Period, the Participant's participation in the Plan
shall terminate and all amounts credited to the Participant's account shall be
paid to the Participant or, in the case of death, to the Participant's heirs or
estate, without interest. Whether a termination of employment has occurred shall
be determined by the Committee. The Committee may also establish rules regarding
when leaves of absence or changes of employment status will be considered to be
a termination of employment, including rules regarding transfer of employment
among Designated Subsidiaries, Subsidiaries and the Corporation, and the
Committee may establish termination of employment procedures for this Plan which
are independent of similar rules established under other benefit plans of the
Corporation and its Subsidiaries.
7. OFFERING.
7.1 Subject to adjustment as set forth in Section 10, the maximum
number of shares of Common Stock which may be issued pursuant to the Plan shall
be 2.5 million shares, plus an annual increase to be added on the last day of
each fiscal year of the Corporation beginning in 2001, equal to one percent (1%)
of the outstanding shares of the Corporation on such date or a lesser amount
determined by the Committee, provided that the maximum number of shares of
Common Stock that may be issued pursuant to the Plan shall be 7.5 million
shares. If, on a given Purchase Date, the number of shares with respect to which
options are to be exercised exceeds the number of shares then available under
the Plan, the Corporation shall make a pro rata allocation of the shares
5
<Page>
remaining available for purchase in as uniform a manner as shall be practicable
and as it shall determine to be equitable.
7.3 With respect to any Offering Period, each eligible Employee who
has elected to participate as provided in Section 5.1 shall be granted, as of
such Employee's Entry Date, an option for each Offering Period to purchase that
number of whole shares of Common Stock (not to exceed 1,500 shares) which may be
purchased with the payroll deductions accumulated on behalf of such Employee
during each such Offering Period at the purchase price specified in Section 7.4
below, subject to the additional limitation that no Employee participating in
the Section 423 Plan shall be granted an option to purchase Common Stock under
the Plan at a rate which exceeds U.S. twenty-five thousand dollars (U.S.
$25,000) of the Fair Market Value of such Common Stock (determined at the time
such option is granted) for each calendar year in which such option is
outstanding at any time. The foregoing sentence shall be interpreted so as to
comply with Code Section 423(b)(8).
7.4 The purchase price under each option shall a percentage (not less
than eighty-five percent (85%)) established by the Committee ("Designated
Percentage") of the Fair Market Value of the Common Stock on the Purchase Date
on which the Common Stock is purchased. The Committee may change the Designated
Percentage with respect to any future Offering Period, but not below eighty-five
percent (85%), and the Committee may determine with respect to any prospective
Offering Period that the option price shall be the Designated Percentage of the
Fair Market Value of the Common Stock on the Purchase Date.
8. PURCHASE OF STOCK.
Upon the expiration of each Offering Period, a Participant's option shall
be exercised automatically for the purchase of that number of whole and
fractional shares of Common Stock which the accumulated payroll deductions
credited to the Participant's account at that time shall purchase at the
applicable price specified in Section 7.4. Notwithstanding the foregoing, the
Corporation or its designee may make such provisions and take such action as it
deems necessary or appropriate for the withholding of taxes and/or social
insurance which the Corporation or its Designated Subsidiary is required by law
or regulation of any governmental authority to withhold. Each Participant,
however, shall be responsible for payment of all individual tax liabilities
arising under the Plan.
9. PAYMENT AND DELIVERY.
As soon as practicable after the exercise of an option, the Corporation
shall deliver to the Participant a record of the Common Stock purchased and the
balance of any amount of payroll deductions credited to the Participant's
account not used for the
6
<Page>
purchase, except as specified below. The Committee may permit or require that
shares be deposited directly with a broker designated by the Committee or to a
designated agent of the Corporation, and the Committee may utilize electronic or
automated methods of share transfer. The Committee may require that shares be
retained with such broker or agent for a designated period of time and/or may
establish other procedures to permit tracking of disqualifying dispositions of
such shares. The Corporation shall retain the amount of payroll deductions used
to purchase Common Stock as full payment for the Common Stock and the Common
Stock shall then be fully paid and non-assessable. No Participant shall have any
voting, dividend, or other Shareholder rights with respect to shares subject to
any option granted under the Plan until the shares subject to the option have
been purchased and delivered to the Participant as provided in this Section 9.
10. RECAPITALIZATION.
If after the grant of an option, but prior to the purchase of Common
Stock under the option, there is any increase or decrease in the number of
outstanding shares of Common Stock because of a stock split, stock dividend,
combination or recapitalization of shares subject to options, the number of
shares to be purchased pursuant to an option, the price per share of Common
Stock covered by an option and the maximum number of shares specified in Section
7.1 may be appropriately adjusted by the Board, and the Board shall take any
further actions which, in the exercise of its discretion, may be necessary or
appropriate under the circumstances.
The Board's determinations under this Section 10 shall be conclusive and
binding on all parties.
11. MERGER, LIQUIDATION, OTHER CORPORATION TRANSACTIONS.
In the event of shareholder approval of a liquidation or dissolution of
the Corporation, the Offering Period will terminate immediately, unless
otherwise provided by the Board in its sole discretion, and all outstanding
options shall automatically terminate and the amounts of all payroll deductions
will be refunded without interest to the Participants.
In the event of a sale of all or substantially all of the assets of the
Corporation, the acquisition by a person (including any entity or group) of
beneficial ownership of a majority of the Corporation's outstanding capital
stock (based on voting power, but excluding any acquisition by the Corporation,
its affiliate, employee benefit plans of the Corporation or its affiliate, and
any underwriter holding securities temporarily pursuant to an offering), or the
merger or consolidation of the Corporation with or into another corporation,
then in the sole discretion of the Board, (1) each option shall be assumed or an
equivalent option shall be substituted by the successor corporation or parent or
subsidiary of such successor corporation, (2) a date established by the Board on
or
7
<Page>
before the date of consummation of such merger, consolidation or sale shall be
treated as a Purchase Date, and all outstanding options shall be exercised on
such date, or (3) all outstanding options shall terminate and the accumulated
payroll deductions will be refunded without interest to the Participants.
12. TRANSFERABILITY.
Options granted to Participants may not be voluntarily or involuntarily
assigned, transferred, pledged, or otherwise disposed of in any way, and any
attempted assignment, transfer, pledge, or other disposition shall be null and
void and without effect. If a Participant in any manner attempts to transfer,
assign or otherwise encumber his or her rights or interests under the Plan,
other than as permitted by the Code, such act shall be treated as an election by
the Participant to discontinue participation in the Plan pursuant to Section
5.2.
13. AMENDMENT OR TERMINATION OF THE PLAN.
13.1 The Plan shall continue until June 30, 2020 unless otherwise
terminated in accordance with Section 13.2.
13.2 The Board may, in its sole discretion, insofar as permitted by
law, terminate or suspend the Plan, or revise or amend it in any respect
whatsoever, except that, without approval of the Shareholders, no such revision
or amendment shall materially increase the number of shares subject to the Plan,
other than an adjustment under Section 10 of the Plan.
14. ADMINISTRATION.
The Board shall appoint a Committee consisting of at least two members
who will serve for such period of time as the Board may specify and whom the
Board may remove at any time. The Committee will have the authority and
responsibility for the day-to-day administration of the Plan, the authority and
responsibility specifically provided in this Plan and any additional duty,
responsibility and authority delegated to the Committee by the Board, which may
include any of the functions assigned to the Board in this Plan. The Committee
may delegate to one or more individuals the day-to-day administration of the
Plan. The Committee shall have full power and authority to promulgate any rules
and regulations which it deems necessary for the proper administration of the
Plan, to interpret the provisions and supervise the administration of the Plan,
to make factual determinations relevant to Plan entitlements and to take all
action in connection with administration of the Plan as it deems necessary or
advisable, consistent with the delegation from the Board. Decisions of the Board
and the Committee shall be final and binding upon all participants. Any decision
reduced to writing and signed by a majority of the members of the Committee
shall be fully effective as if it had been made at a meeting of the Committee
duly held. The
8
<Page>
Corporation shall pay all expenses incurred in the administration of the Plan.
No Board or Committee member shall be liable for any action or determination
made in good faith with respect to the Plan or any option granted hereunder.
15. COMMITTEE RULES FOR FOREIGN JURISDICTIONS.
The Committee may adopt rules or procedures relating to the operation and
administration of the Plan to accommodate the specific requirements of local
laws and procedures. Without limiting the generality of the foregoing, the
Committee is specifically authorized to adopt rules and procedures regarding
handling of payroll deductions, payment of interest, conversion of local
currency, payroll tax, withholding procedures and handling of stock certificates
which vary with local requirements.
The Committee may also adopt "sub-plans" separate from this Plan for
purposes of Code Section 423 applicable to particular affiliates of the
Corporation, which sub-plans may be designed to be outside the scope of Code
section 423. Notwithstanding the foregoing, the shares of Common Stock issued
under any sub-plan shall be aggregated with the shares of Common Stock issued
under this Plan and such aggregate number of shares shall be subject to the
maximum number set forth under Section 7.1 hereof. The rules of such sub-plans
may take precedence over other provisions of this Plan, with the exception of
Section 7.1, but unless otherwise superseded by the terms of such sub-plan, the
provisions of this Plan shall govern the operation of such sub-plan.
16. SECURITIES LAWS REQUIREMENTS.
The Corporation shall not be under any obligation to issue Common Stock
upon the exercise of any option unless and until the Corporation has determined
that: (i) it and the Participant have taken all actions required to register the
Common Stock under the Securities Act of 1933, or to perfect an exemption from
the registration requirements thereof; (ii) any applicable listing requirement
of any stock exchange on which the Common Stock is listed has been satisfied;
and (iii) all other applicable provisions of state, federal and applicable
foreign law have been satisfied.
17. GOVERNMENTAL REGULATIONS.
This Plan and the Corporation's obligation to sell and deliver shares of
its stock under the Plan shall be subject to the approval of any governmental
authority required in connection with the Plan or the authorization, issuance,
sale, or delivery of stock hereunder.
18. NO ENLARGEMENT OF EMPLOYEE RIGHTS.
Nothing contained in this Plan shall be deemed to give any Employee
the right to be retained in the employ of the Corporation or any Designated
Subsidiary or to interfere with the right of the Corporation or Designated
Subsidiary to discharge any Employee at any time.
9
<Page>
19. GOVERNING LAW.
This Plan shall be governed by Delaware law, without regard to that
State's choice of law rules.
20. EFFECTIVE DATE.
This Plan was adopted by the Corporation's Board of Directors on June 9,
2000, was approved by the sole shareholder of the Corporation on June 9, 2000,
and became effective on July 10, 2000. The amendments to the Plan adopted by the
Board of Directors on January 27, 2005 shall become effective for Offering
Periods commencing on or after July 1, 2005.
21. REPORTS.
Individual accounts shall be maintained for each Participant in the Plan.
Statements of account shall be given to Participants at least annually, which
statements shall set forth the amounts of payroll deductions, the Purchase
Price, the number of shares purchased and the remaining cash balance, if any.
10