Innoviva (INVA) 8-K Regulation FD Disclosure

 CorporatePresentation  April 2022 

 Important information  On March 25, 2022, the Company filed a Definitive Proxy Statement on Schedule 14A and accompanying proxy card with the Securities and Exchange Commission (“SEC”) to be used to in connection with the Company’s 2022 annual meeting of the stockholders.THE COMPANY STRONGLY ADVISE ALL STOCKHOLDERS OF THE COMPANY TO READ THE PROXY STATEMENT AND OTHER PROXY MATERIALS (IF ANY) AS THEY BECOME AVAILABLE BECAUSE THEY CONTAIN IMPORTANT INFORMATION. SUCH PROXY MATERIALS WILL BE AVAILABLE AT NO CHARGE ON THE SEC’S WEB SITE AT HTTP://WWW.SEC.GOV. IN ADDITION, THE COMPANY WILL PROVIDE COPIES OF THE PROXY STATEMENT WITHOUT CHARGE UPON REQUEST.  2 

 Forward-looking statements  The information in this presentation contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended (“Securities Act”), and Section 21E of the Securities Exchange Act of 1934, as amended. Such forward-looking statements involve substantial risks, uncertainties, and assumptions. All statements contained herein that are not of historical fact, including, without limitation, statements regarding our strategy, future operations, future financial position, future revenue, projected costs, prospects, plans, intentions, expectations, goals and objectives, may be forward-looking statements. The words “anticipates,” “believes,” “could,” “designed,” “estimates,” “expects,” “goal,” “intends,” “may,” “objective,” “plans,” “projects,” “pursue,” “will,” “would” and similar expressions (including the negatives thereof) are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions, expectations or objectives disclosed in our forward-looking statements and the assumptions underlying our forward-looking statements may prove incorrect. Furthermore, if our forward-looking statements prove to be inaccurate, the inaccuracy may be material. Therefore, you should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions, expectations and objectives disclosed in the forward-looking statements that we make. All forward-looking statements attributable to us or any person acting on our behalf are expressly qualified in their entirety by the cautionary statements contained or referred to in this section. Important factors that we believe could cause actual results or events to differ materially from our forward-looking statements include, but are not limited to, risks related to: lower than expected future royalty revenue from respiratory products partnered with GSK; the commercialization of RELVAR®/BREO® ELLIPTA®, ANORO® ELLIPTA® and TRELEGY® ELLIPTA® in the jurisdictions in which these products have been approved; substantial competition from products discovered, developed, launched and commercialized both by GSK and by other pharmaceutical companies; our strategies, plans and objectives (related to our growth strategy and corporate development initiatives beyond our existing portfolio); the timing, manner and amount of capital deployment, including potential capital returns to stockholders; risks related our growth strategy; projections of revenue, expenses and other financial items. In light of the significant uncertainties in these forward-looking statements, you should not regard these statements as a representation or warranty by us or any other person that we will achieve our objectives and plans in any specified time frame, or at all. Any person reviewing this presentation is advised to review our “Risk Factors” and other information in our Annual Report on Form 10-K for the year ended December 31, 2021 filed with the Securities and Exchange Commission (“SEC”) on February 28, 2022, (“2021 Form 10-K”), and the information in the other reports and documents that we file with the SEC from time to time. All information in this presentation should be read in conjunction with the information we have filed with the SEC. All forward-looking statements in this presentation are based on current expectations as of the date hereof and we do not assume any obligation to update any forward-looking statements on account of new information, future events or otherwise.  3 

 Innoviva overview    Company highlights    Diversified holding company with a portfolio of royalties and a growing portfolio of innovative healthcare investments and assetsRoyalty portfolio consists of respiratory products that were jointly developed with, and are licensed to, GSK and collectively make up the majority of GSK’s leading respiratory franchise (RELVAR®/ BREO® ELLIPTA®, ANORO® ELLIPTA®, TRELEGY® ELLIPTA®)Strategic healthcare investments – investments in areas with high unmet medical need and significant long-term value creation potential, oftentimes with a focus on control positions  3  Thoughtful, robust approach to capital deployment with long-term horizon      5  Efficient and flexible platform enabling meaningful, sustainable value generation      4  Strong track record of growth and unrelenting value creation focus      2  Deep and proven healthcare expertise across governance, strategy, R&D, finance, and operations      1  Strongly cashflow-generative, diversified and durable core royalty business        4  Company description   

 Innoviva combines sustainable royalty cashflows with a long-term capital deployment strategy to drive innovation and maximize shareholder value    Robust, valuable royalty portfolio  Thoughtful, accretive capital deployment  Long-term shareholder value creation      +  =  Significant royalties from a durable and growing portfolio of blockbuster respiratory products  Strategic healthcare asset acquisitions and capital structure optimization to drive sustainable growth  Strong record of growth and capital deployment position the company for continued value creation  5  Over $250M net income to Innoviva stockholders generated in 2021 

 Innoviva has a valuable royalty portfolio comprised of robust, durable revenues stemming from widely used respiratory therapies commercialized by GSK    2021 Global net sales ($B)  Key royalty terms  2021 Innoviva royalties1 ($M)  Totals  15% on first $3B in annual sales; 5% on sales over $3B 100% economics  Tiered 6.5-10.0%100% economics  Tiered 6.5-10.0%15% economics1  5-year projected royalties1,2 ($B)  ANORO®ELLIPTA®  RELVAR®/ BREO®ELLIPTA®  TRELEGY®ELLIPTA®  1 – TRELEGY® ELLIPTA® royalties are assigned to Theravance Respiratory Company LLC, a subsidiary of Innoviva, where Theravance Biopharma holds 85% economic interest; 100% royalty economics shown2 – Projections per analyst consensus on GSK forecast website accessed March 28, 2022; GBP converted to USD using March 28 exchange rate of $1.31; 2022-2026E royalties shown     $3.9B  $406M  ~$2.4B  6  Royalty portfolio  Asthma / COPD  COPD  Asthma / COPD 

 Our royalty product portfolio has demonstrated resilience and growth; we remain excited about its long-term potential while we build out the next generation of high impact products    Sizeable and differentiated  Resilient anddurable  Diversifiedand growing  Differentiated respiratory therapies portfolio with over $3B annual salesConsensus projections imply royalties of $2B+ over the next 5 years1  Robust products have performed well across environments despite competitive pressuresMeaningful longevity afforded by strong IP estate, with the “moat” amplified by manufacturing complexity  Broad portfolio covers all major respiratory drug classes in easy-to-use single daily dose formPortfolio contains products across the life cycle, including relatively mature standard of care therapies (RELVAR®/ BREO® ELLIPTA®, ANORO® ELLIPTA®) and fast-growing innovative products (TRELEGY® ELLIPTA®)Products approved and launching in multiple geographies and indications, reducing single-market risk  1 – Projections per analyst consensus on GSK forecast website accessed March 28, 2022; GBP converted to USD using March 28 exchange rate of $1.31; 100% Trelegy royalties included; 2022-2026E  7  Royalty portfolio 

 Innoviva actively deploys its capital to maximize shareholder value    In 2021 we strategically repurchased GSK’s equity stake for ~$400M and continued to deploy capital into high-potential assets – with ~$480M equity and investments on the balance sheet at year-end  Continued active search for strategically attractive opportunities with external supportLong-term, deliberate approach to direct strategic investments into promising healthcare assets, matching the meaningful duration of our cashflowsConcentrated exposure to fundamentally robust, attractively priced assets with significant upsidePotential capital return to shareholders as appropriate, especially when strong economic value accretion is coupled with compelling strategic benefitsE.g., GSK’s 32% equity stake repurchase in May 2021 at $12.25 per share for $392M1  We thoughtfully approach capital deployment with a strong value focus  8  1 – Excludes associated feesNote: $484M equity and long-term investments assets on balance sheet as of Dec 31, 2021.   Capital deployment 

 We approach strategic transactions in a thoughtful and disciplined manner    We target fundamentally attractive, yet often overlooked or contrarian, healthcare areas where our capital and capabilities can make a difference We look for differentiated assets with meaningful value creation potential  We structure and negotiate asset acquisitions on mutually beneficial terms to maximize long-term valueFocus on concentrated, long-term investments, often by purchasing majority or other large stakesOpenness to smaller investments in companies with compelling growth and risk profiles We proactively manage risks through ongoing asset stewardship and appropriate diversificationOperational and strategic support (across strategy, finance, development, commercial, governance, and other areas) as a key value creation driver  Opportunity identification  Strategic investment execution  9  Capital deployment 

 Strategic investment case study: infectious disease    Infectious disease therapeutics have focused primarily on common bacteria diseases; however, there is a clear need for improved therapeutics for specific bacterial diseases, along with viral and fungal diseasesIdiosyncratic challenges leading to historical underinvestment have resulted in compelling strategic opportunitiesA player with long-term vision, capital, and expertise can take advantage of market dislocations and facilitate R&D and commercialization of novel, differentiated treatments capable of generating significant value for patients and health systems – and producing strong returns  Infectious disease is a promising area of high unmet medical need with currently scarce capital access  Selected Innoviva transactions (end-2021)  Pathogen-specific bacteriophage therapeutics platform for the treatment of drug resistant infections and other usesHighly differentiated novel biologic platform with broad applicability, rooted in a well-known modality and supported by strong manufacturing capabilitiesBroad development program with lead therapy focused on respiratory Pseudomonas aeruginosa infections in cystic fibrosis patients, an area of high unmet need  Novel antibacterial platform validated by lead asset’s highly differentiated profile in an area of unmet needNovel potential carbapenem-resistant Acinetobacter treatment SUL-DUR has significant commercial promise following favorable efficacy and safety in pivotal trialOngoing Phase 3 trial for gonorrhea antibiotic“Rational design” platform used to develop earlier stage antibiotics less susceptible to resistance  $68M cost basis1  ~60% ownership1  $49M cost basis1  ~60% ownership1  $104M fair value1  $147M fair value1  1 – As of Dec 31, 2021. On February 1, 2022, Innoviva made an initial non-binding offer to acquire Entasis and made $15M investment on February 18, 2022; on March 15, 2022, Innoviva revised the non-binding Entasis offer. On February 9, 2022, Innoviva announced $45M investment in Armata, $18.1 million of which closed on February 9, 2022, and the remainder on March 31, 2022  10  Capital deployment 

 Innoviva is the sole manager of all TRELEGY®ELLIPTA® royalties via TRC, seeking to maximize long-term equity holder value    11  1 – Projections per analyst consensus on GSK forecast website accessed March 28, 2022; GBP converted to USD using March 28 exchange rate of $1.31; 100% Trelegy royalties included; 2022-2026E  An Innoviva subsidiary, Theravance Respiratory Company LLC (TRC), receives all TRELEGY® ELLIPTA® royalties from GSK$127M in 2021 with approximately $1.1B projected over 5 years based on consensus estimates1Innoviva as Manager of TRC has a broad mandate and responsibility to maximize the value of TRC both by active management of the TRELEGY® ELLIPTA® royalties and via strategic investmentsUltimately, 15% economics accrue to Innoviva (and 85% to Theravance Biopharma)Theravance Biopharma unsuccessfully challenged our ability to make investments in arbitrationAdditional active strategic investing anticipated seeking significant value creation with uncertainty removed (due to the successful resolution of the Theravance Biopharma arbitration) in light of strong current opportunity set, benefiting from our long-term orientation  Additional detail in the appendix  Capital deployment 

     Relevant experience    Management Team  Pavel Raifeld, CFAChief Executive Officer  Experienced finance and life sciences professional; formerly with Sarissa Capital, Credit Suisse, McKinsey and BCG      Marianne Zhen, CPAChief Accounting Officer  Experienced finance professional with over 20 years in accounting and strategic operations    Board of Directors  George Bickerstaff,Chairperson  Managing Director at M.M. Dillon & Co.; former CFO of Novartis Pharma AG and IMS Health; director at CareDx      Deborah L. Birx, M.D.  Physician-scientist and healthcare leader; former response coordinator of The White House Coronavirus Task Force      Mark DiPaolo, Esq.  Senior Partner and General Counsel at Sarissa Capital; former senior member Icahn Capital’s investment team      Jules Haimovitz  Founder, executive, and director of multiple companies in life sciences and entertainment; former director of Ariad Pharma      Odysseas Kostas, M.D.  Senior Managing Director at Sarissa Capital; former life sciences analyst at Evercore ISI and practicing physician      Sarah J. Schlesinger, M.D.  Professor at Rockefeller University with governance and clinical / medical expertise; former director of The Medicines Company and Ariad Pharma    Innoviva’s management and board have world-class expertise in healthcare and single-minded focus on value creation – brought to bear for the benefit of shareholders  Innoviva Team    (Icahn Capital)  12  Joined in 2021  World-class expertise  Unique and complementary skill sets  Strong value creation focus  Proven track record of success  Value creation   

 2021 was a milestone year both in terms of financial performance and strengthening our operating platform  $406M total royalty revenues$364M net cash provided by operating activities$3.24 basic net income per share2$266M net income  13    Value creation  Strategically deployed over $450M in 2021Accretively repurchased GSK’s 32% equity stake for $392M3 (at $12.25 per share)Strategically invested $~65M into innovative healthcare assetsStrengthened Innoviva platformAdded healthcare and infectious disease leader Deborah L. Birx to the BoardIn 20224, continued to strategically deploy capital and improve capital structureInvested $~70M into healthcare assetsIssued $261M 2.125% convertible notes due 2028, partially using proceeds to retire a portion of 2023 notes  23% CAGR  Financial highlights (2021)  Business highlights  1 – Includes 100% TRELEGY® ELLIPTA® royalties2 – $2.87 diluted net income per share; attributable to Innoviva stockholders3 – Excludes associated fees4 – 1Q2022 data shown 

   Why Innoviva    5  Efficient and flexible platform enabling meaningful, sustainable value generation    4  Strong track record of growth and unrelenting value creation focus    3  Thoughtful, robust approach to capital deployment with long-term horizon    2  Deep and proven healthcare expertise – across governance, strategy, R&D, commercial, finance, and operations – brought to bear across everything we do    1  Strongly cashflow-generative, diversified and durable core royalty business   14    Value creation 

 Appendix  15 

     RELVAR®/BREO® ELLIPTA® detail: First once-daily inhaled corticosteroid / long-acting beta-agonist for asthma and chronic obstructive pulmonary disease    RELVAR® / BREO®ELLIPTA®  Launched in 2013 as first and only once-daily ICS / LABA in the U.S.RELVAR®/ BREO® ELLIPTA® delivers superior, lasting proactive asthma control, with simple once-daily dosing in an easy-to-use deviceHistorical resilience in a competitive, volatile environment supported by positive demographic trends  Net global sales ($B)  Implied royalties ($M)  (fluticasone furoate 100 mcg and vilanterol 25 mcg inhalation powder)  Indications (US)Long-term, once-daily, maintenance treatment of airflow obstruction and reducing exacerbations in patients with COPDOnce-daily treatment of asthma in patients aged 18 years and older  1  1 – Projections per analyst consensus on GSK forecast website accessed March 28, 2022; GBP converted to USD using March 28 exchange rate of $1.31  16  100% economics to INVA  Royalty portfolio 

   ANORO® ELLIPTA® detail: Best-in-class long-acting beta-agonist / long-acting muscarinic antagonist for COPD    ANORO®ELLIPTA®  (umeclidinium 62.5 mcg and vilanterol 25 mcg inhalation powder)  Indications (US)Long-term, once-daily, maintenance treatment of airflow obstruction and reducing exacerbations in patients with COPD  Net global sales ($B)  Implied royalties ($M)  1 – Projections per analyst consensus on GSK forecast website accessed March 28, 2022; GBP converted to USD using March 28 exchange rate of $1.312 – Superior improvement in lung function has been demonstrated in clinical trials of ANORO® ELLIPTA® vs. Tiotropium (LAMA) and Spiolto (LAMA/LABA)  17  1    Launched in 2014 as first-in-class LABA / LAMA single inhaler product in the U.S.ANORO® ELLIPTA® delivers superior lung function improvement vs common initial maintenance therapy options2Class leader in the U.S. due to clear differentiationLong-term prospects supported by positive demographics  100% economics to INVA  Royalty portfolio 

   TRELEGY® ELLIPTA® detail: First 3-in-1 inhaled corticosteroid / long-acting beta-agonist / long-acting muscarinic antagonist for COPD and asthma    TRELEGY®ELLIPTA®  Net global sales ($B)  Implied royalties ($M)  (fluticasone furoate 100 mcg, umeclidinium 62.5 mcg and vilanterol 25 mcg inhalation powder)  Indications (US)Long-term, once-daily, maintenance treatment of patients with COPD, including chronic bronchitis and/or emphysemaOnce-daily treatment of asthma in patients aged 18 years and older  18  1 – Projections per analyst consensus on GSK forecast website accessed March 28, 2022; GBP converted to USD using March 28 exchange rate of $1.312 – FULFIL trial vs. Symbicort (ICS/LABA), IMPACT study vs. ICS/LABA and LAMA/LABA3 – TRELEGY® ELLIPTA® royalties are assigned to Theravance Respiratory Company LLC, a subsidiary of Innoviva, where Theravance Biopharma holds 85% economic interest; 100% royalty economics shown  1    Launched in 2017 as first-in-class ICS / LABA / LAMA single inhaler product in the U.S.TRELEGY® ELLIPTA® demonstrated superior efficacy in clinical trials for COPD vs double combination drug classes2Strong growth driven by demographic tailwinds, increasing class adoption, and share increase across geographies   15% economics to INVA3  Royalty portfolio 

   GSK net global sales1 ($B)    Net global sales and royalty revenues have grown over time  Innoviva Royalty Revenue2 ($M)    Note: May not sum due to rounding1 – Reflects net sales from RELVAR®/ BREO® ELLIPTA®, ANORO® ELLIPTA®, TRELEGY® ELLIPTA®2 – Excludes the impacts of amortization of capitalized fees and the MABA strategic alliance; reflects TRELEGY® ELLIPTA® royalties received by TRC at 100%; may not sum due to rounding  TRELEGY® ELLIPTA® Royalties @ 15% Economics  -  -  $2mm  $6mm  $11mm  $19mm  19  ’16 – ’21 CAGR: 28%  ’16 – ’21 CAGR: 23%    Royalty portfolio 

 Innoviva’s portfolio products are protected by a robust IP estate with meaningful remaining exclusivity  Manufacturing complexity provides further protection  Primary US patent  ANORO®ELLIPTA®  RELVAR®/ BREO®ELLIPTA®  TRELEGY®ELLIPTA®  Potential expiration  Key secondary US patent  Potential expiration  Vilanterol drug substance1   ELLIPTA device4  Specified LABA/LAMA combination for treatment of COPD and asthma2,3  Process for aggregating particles of umeclidinium and/or vilanterol and/or fluticasone furoate5  Specified LABA/LAMA combination for treatment of COPD and asthma2,3  1 – US patent 7439393. Original expiration 9/11/2022, granted additional exclusivity to May 2025 through 35 USC §1562 – US patents 9750726 and 110902943 – Umeclidinium (contained in Anoro and Trelegy) is covered by US drug substance patent 7488827; original expiration 4/27/2025, granted extension to Dec 2027 through 35 USC §156 4 – US patent 87462425 – US patent 9763965  2025  2030  2030  Process for aggregating particles of umeclidinium and/or vilanterol and/or fluticasone furoate5  2030  2033  2033    The terms of the collaboration agreement with GSK indicate that royalties will be paid until the later of:The expiration of the last patent covering each product in such country 15 years from first commercial sale of each product in such countryFor each of the portfolio products, the secondary patent expiration date would be the later date for purposes of royaltiesIP protection in international markets is generally longer dated than in the US  20    Royalty portfolio 

 Additional TRC information  While TRC actively manages its royalty-producing relationship with GSK, under the LLC Agreement, TRC is permitted to “engage in any lawful business”; additionally, Innoviva was granted broad “decision-making authority as to the LLC”There have been two separate arbitrations brought by Theravance Biopharma against Innoviva and TRC over the last two years challenging the scope of Innoviva’s authority as Manager of TRC to deploy capital rather than simply distribute royalty incomeThe arbitrator ruled in favor of Innoviva and TRC in both arbitrations. The arbitrator has confirmed that the LLC Agreement broadly empowers the LLC to engage in any lawful business and that Innoviva has the “discretion” and “freedom” under the LLC Agreement to determine how to use the LLC’s cash, including in investments unrelated to TRELEGY® ELLIPTA®. The arbitrator did not enjoin TRC from making additional investmentsEach of the arbitrator’s decisions is publicly available  Arbitration background  Example investments  InCarda focuses on cardiovascular diseases; its lead drug is in late-stage development for large, attractive PAF1 market  ImaginAb is a leader in radio-pharmaceutical imaging with a differentiated solution for IO2 patient care and other areas of unmet medical need  21  1 – Paroxysmal atrial fibrillation2 – Immuno-oncology  Gate Neurosciences is developing next-generation therapies for psychiatric and neurological disorders  Nanolive is a microscopy company that has developed a method for live cell 3D imaging and analysis with applications across drug discovery and biotech R&D    Capital deployment 

 Innoviva’s platform optimizes for lean, focused value creation leveraging superior capabilities  Low-cost, efficient operating platform  Best-in-class internal capabilities  Superior external resources access  Our key operations principles are cost discipline, flexibility, and value orientation, while ensuring we are well-resourced to executeLean expense structure; 2021 G&A expense totaled ~$16MFlexibility and scalability are key Strong revenue conversion to income and cashflows  Management team and board members have significant functional and industry expertise with proven track records in key areas utilized both at Innoviva and our investeesMedicine, science, and R&D; M&A and investments; governance and management; strategy and planning; commercial and operations  Deep, multi-year relationships across healthcare ecosystem enabling differentiated deal flow and talent pool accessExternal advisors, investment community, industry, government, patient groups, and others    Innoviva is well positioned for strong execution  22    Value creation