A Note from Phathom’s CEO To Our Shareholders: After a year of unparalleled challenges, I hope that this letter finds you and your loved ones healthy and safe. The unforeseen personal and professional difficulties endured by many due to the COVID-19 pandemic pale in comparison to the millions of lives lost. Thanks to the relentless efforts of the healthcare community, including the groundbreaking development and distribution of lifesaving vaccines and treatments by our own pharmaceutical industry, there is a renewed hope and optimism that the end of the pandemic is in sight. Phathom, like so many others, faced uncertainties and significant challenges in 2020 due to COVID-19, including a three month pause in patient enrollment in our Phase 3 trials. The demands on medical institutions and clinicians during the beginning of the crisis, coupled with the safety of study participants and Phathom staff, made this the most prudent decision. Despite the obstacles 2020 presented, our teams rose to the challenge–showcasing Phathom’s culture of resilience and our unwavering commitment to meet the unmet needs of patients suffering from acid-related diseases. Last year, we completed and exceeded our enrollment target of 1,000 patients in our pivotal Phase 3 trial for vonoprazan in erosive esophagitis (PHALCON-EE) and achieved our target patient enrollment in our pivotal Phase 3 trial for vonoprazan in H. pylori infection (PHALCON-HP)–completing and again exceeding patient enrollment in January 2021. The progress made last year advancing the clinical development of vonoprazan, a potassium competitive acid blocker (P-CAB), demonstrates the urgent need for new therapeutic options for patients suffering from erosive esophagitis andH. pylori infection. In addition to completing patient enrollment in our two pivotal Phase 3 trials, some of our most important 2020 accomplishments and recent business highlights include: • Recruitment of seasoned industry professionals and dynamic leaders, including the build-out of our medical, commercial, marketing, sales, and support functions. • Announcement of plans to expand the vonoprazan development program into non-erosive reflux disease (NERD), a major subcategory of gastroesophageal reflux disease (GERD). • Build out of the commercial supply chain to support the planned H. pylori NDA submission and launch readiness. • Agreement with the FDA and European Medicines Agency regarding plans for our vonoprazan pediatric programs. • Further strengthening the Board of Directors with the appointment of commercial veteran Mark Stenhouse, Chief Operating Officer of Prometheus Biosciences. • A follow-on offering of common stock with net proceeds of approximately $89 million to fund the clinical develop- ment of vonoprazan and for working capital and general corporate purposes, including pre-commercial activities. The continued commercial success of vonoprazan in markets outside of the US, Europe, and Canada underscores the poten- tial of vonoprazan to be the first gastric anti-secretory agent from a novel class approved in the United States, Europe, or Can- ada in over 30 years. To date, vonoprazan has been studied in 19 Phase 3 clinical trials and is approved in fourteen countries across Asia and Latin America. In Japan, the market where vonoprazan was first approved, vonoprazan is the sales leader among acid-reducing agents and vonoprazan-based regimens are used to treat over 80% of patients with H. pylori infection. As we look forward to the remainder of 2021, we will build upon our progress from 2020 and deliver our key milestones. Our primary focus will be on the expected results from our pivotal Phase 3 trials in H. pylori infection and erosive esophagitis, initiation of our NERD development program, and preparation of a potential regulatory submission for H. pylori infection with the FDA. Our determination to bring vonoprazan to millions of underserved patients with gastrointestinal diseases remains steadfast, and our excitement is building as we continue to advance our mission to change the landscape in gastrointestinal diseases. On behalf of the entire Phathom Team, thank you for your continued support and your commitment to our mission moving forward. We look forward to updating you on our progress throughout the year. Sincerely, Terrie Curran President & Chief Executive Officer UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-K (Mark One) ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ☒ ACT OF 1934 For the fiscal year ended December 31, 2020 OR TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ☐ ACT OF 1934 For the transition period from to Commission file number: 001-39094 PHATHOM PHARMACEUTICALS, INC. (Exact name of Registrant as specified in its charter) Delaware 82-4151574 (State or Other Jurisdiction of (I.R.S. Employer Incorporation or Organization) Identification No.) 100 Campus Drive, Suite 102 Florham Park, New Jersey 07932 (Address of Principal Executive Offices) (Zip Code) Registrant’s Telephone Number, Including Area Code: (877) 742-8466 Securities registered pursuant to Section 12(b) of the Act: Title of each class Trading Symbol(s) Name of each exchange on which registered Common Stock, par value $0.0001 per share PHAT The Nasdaq Global Select Market Securities registered pursuant to Section 12(g) of the Act: None Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes ☐ No ☒ Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes ☐ No ☒ Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐ Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No ☐ Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act. Large accelerated filer Accelerated filer ☐ ☐ Non-accelerated filer Smaller reporting company ☒ ☒ Emerging growth company ☒ If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☒ Indicate by check mark whether the registrant has filed a report on and attestation to its management’s assessment of the effectiveness of its internal control over financial reporting under Section 404(b) of the Sarbanes Oxley Act (15 U.S.C. 7262 (b)) by the registered public accounting firm that prepared or issued its audit report. ☐ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act). Yes ☐ No ☒ As of June 30, 2020, the aggregate market value of the registrant’s common stock held by non-affiliates of the registrant was approximately $552.3 million, based on the closing price of the registrant’s common stock on the Nasdaq Global Select Market of $32.91 per share. As of March 26, 2021, the registrant had 31,321,613 shares of common stock ($0.0001 par value) outstanding. DOCUMENTS INCORPORATED BY REFERENCE Certain sections of the registrant’s definitive proxy statement for the 2021 annual meeting of stockholders to be filed with the Securities and Exchange Commission pursuant to Regulation 14A not later than 120 days after the end of the fiscal year covered by this Form 10-K are incorporated by reference into Part III of this Form 10-K. PHATHOM PHARMACEUTICALS, INC. TABLE OF CONTENTS FORM 10-K For the Year Ended December 31, 2020 INDEX PART I Item 1. Business 4 Item 1A. Risk Factors 47 Item 1B. Unresolved Staff Comments 105 Item 2. Properties 105 Item 3. Legal Proceedings 105 Item 4. Mine Safety Disclosures 105 PART II Item 5. Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities 106 Item 6. Selected Financial Data 108 Item 7. Management’s Discussion and Analysis of Financial Condition and Results of Operations 109 Item 7A. Quantitative and Qualitative Disclosures About Market Risk 122 Item 8. Financial Statements and Supplementary Data 122 Item 9. Changes in and Disagreements with Accountants on Accounting and Financial Disclosure 122 Item 9A. Controls and Procedures 122 Item 9B. Other Information 123 PART III Item 10. Directors, Executive Officers and Corporate Governance 124 Item 11. Executive Compensation 124 Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters 124 Item 13. Certain Relationships and Related Transactions, and Director Independence 124 Item 14. Principal Accounting Fees and Services 124 PART IV Item 15. Exhibits, Financial Statement Schedules 125 Item 16. Form 10-K Summary 125 Signatures