Financial Performance - The company incurred a net loss of $201.6 million for the year ended December 31, 2023, compared to a net loss of $197.7 million for 2022, with an accumulated deficit of $928.7 million as of December 31, 2023[311]. - The company expects to continue incurring significant operating losses for the foreseeable future, with uncertainty regarding achieving profitability[311][312]. - The company anticipates that existing cash and cash equivalents, along with a remaining $160 million drawdown under its loan agreement, will fund operations for at least the next 12 months and through the end of 2026[316]. Product Development and Commercialization - The company relies entirely on the success of its recently launched products: VOQUEZNA, VOQUEZNA TRIPLE PAK, and VOQUEZNA DUAL PAK, which were introduced in Q4 2023[308]. - The successful commercialization of its products will depend on obtaining adequate reimbursement and favorable pricing policies from governmental authorities and health insurers[310]. - The commercialization of VOQUEZNA, VOQUEZNA TRIPLE PAK, and VOQUEZNA DUAL PAK is dependent on the company's marketing, sales, and distribution capabilities, which were only developed in late 2023 due to prior delays[322]. - The company has limited experience in commercializing products, which may hinder its ability to successfully market its product candidates[308]. - The company faces uncertainty regarding third-party payer coverage and reimbursement, which is essential for patient access to products like VOQUEZNA[335]. Regulatory and Compliance Risks - The company faces risks related to regulatory approvals and the potential for delays in clinical trials, which could impact its product pipeline[310][318]. - The FDA and other regulatory authorities may impose ongoing requirements for post-approval studies and surveillance, leading to significant additional expenses for the company[323]. - The company must comply with the Medicaid Drug Rebate Program, which imposes extensive reporting obligations and penalties for non-compliance[342]. - The ongoing review of EU pharmaceutical legislation may significantly impact the company's business and regulatory environment in the long term[327]. - The company must comply with various regulatory requirements for drug approval in foreign markets, which may pose additional risks[361]. Financial Obligations and Funding - The company is required to make milestone and royalty payments to Takeda, which could impact its financial position and operational capabilities[314]. - The company has entered into a Loan Agreement with Hercules, borrowing $100 million initially and an additional $40 million in December 2023, with a total borrowing capacity of up to $260 million[434]. - Under the Revenue Interest Financing Agreement, the company can receive up to $300 million in funding, with $175 million received following FDA approval of vonoprazan for Erosive GERD treatment[438]. - Investors under the Revenue Interest Financing Agreement are entitled to a 10% royalty on net sales of products containing vonoprazan, with a step-down on exceeding certain annual thresholds[439]. Market Competition - The company faces significant competition from larger pharmaceutical firms and research institutions, which may adversely affect its ability to develop and commercialize products[349]. - The company expects VOQUEZNA to compete primarily with generic PPIs in both prescription and OTC markets, as well as with Talicia for H. pylori infection treatment[350]. - The company is aware of multiple competitors developing similar products, including Daewoong and Cinclus, which may launch products in the near future[351]. Clinical Trials and Development Challenges - The company faces risks related to delays in clinical trials, regulatory approvals, and potential adverse events that could impact the commercialization of vonoprazan[366]. - The timeline for recruiting patients and conducting trials may be significantly delayed if a sufficient number of patients cannot be enrolled[384]. - The company must conduct extensive clinical trials to demonstrate the safety and efficacy of vonoprazan for new indications before obtaining marketing approvals[375]. - Delays in clinical trials could increase costs and hinder the ability to generate revenue from vonoprazan and future product candidates[380]. Intellectual Property and Licensing - The company relies on the Takeda License for exclusive rights to develop and commercialize vonoprazan in the United States, Europe, and Canada, with potential termination risks impacting business prospects[411]. - The company has in-licensed patents related to vonoprazan from Takeda, but currently does not own any issued patents or pending patent applications[479]. - There is uncertainty regarding the ability to enforce pending patent applications, which may not result in issued patents providing sufficient protection[480]. - The patent position of biopharmaceutical companies is highly uncertain, affecting the commercial value of patent rights[492]. Legal and Regulatory Compliance - The company is subject to the U.S. federal Anti-Kickback Statute and other laws that impose strict penalties for non-compliance, which could include exclusion from government healthcare programs[446]. - The company may face civil and criminal penalties for noncompliance with healthcare and data privacy laws, impacting operations and profitability[475]. - The company is subject to the EU GDPR, which imposes fines of up to €20 million or 4% of annual global revenues for noncompliance[469]. Operational Risks - The company faces risks related to epidemic diseases, such as COVID-19, which could disrupt business activities and supply chains, impacting clinical trials and commercialization efforts[432]. - The company anticipates challenges in managing growth due to limited experience in handling significant operational expansion[444]. - The company must maintain certain financial covenants under its Loan Agreement, which could limit operational flexibility and expose it to default risks[436].

Financial Data and Key Metrics Changes - For Q4 2023, the company reported net revenues of $682,000, reflecting initial stocking of wholesalers in December, with VOQUEZNA becoming commercially available on November 28 [11][24] - Gross profit for Q4 2023 was $515,000, resulting in a gross margin of approximately 76% [11] - GAAP net loss for Q4 2023 was $79.6 million, or $1.39 loss per share, compared to a loss of $55 million, or $1.33 loss per share in Q4 2022 [12] - Non-GAAP adjusted net loss for Q4 2023 was $46 million, or $0.80 loss per share, compared to $42.2 million, or $1.02 loss per share in the same period of 2022 [12] - As of December 31, 2023, cash and cash equivalents were $381 million, including $175 million received from a revenue interest financing agreement [12][41] Business Line Data and Key Metrics Changes - The company reported over 3,800 filled prescriptions for VOQUEZNA as of February 23, 2024, with an estimated total of 14,000 prescriptions written since launch [8][18] - The sales force's efforts have resulted in over 1,200 unique prescribers writing VOQUEZNA scripts, with repeat prescribing observed [8][10] Market Data and Key Metrics Changes - VOQUEZNA's total commercial coverage now reflects an estimated 60 million commercially covered lives, following its addition to Express Scripts' national formularies [22][51] - The company anticipates that the gap between total demand and filled scripts will narrow significantly as payer access improves [6][9] Company Strategy and Development Direction - The company aims to become the number one prescribed acid suppressant in the U.S. and is focused on expanding market access and driving demand for VOQUEZNA [7][34] - The FDA has accepted the NDA for non-erosive GERD daily dosing, with a target action date of July 19, 2024, which could significantly broaden VOQUEZNA's addressable population [6][34] - A new branded consumer campaign targeting Erosive GERD patients is set to launch, including TV commercials on popular streaming services [23] Management's Comments on Operating Environment and Future Outlook - Management expressed confidence in the strong demand for VOQUEZNA, citing positive feedback from physicians and patients [5][34] - The company believes that the successful launch and ongoing negotiations with payers will lead to increased filled prescriptions throughout 2024 [55][56] - Management highlighted the potential for VOQUEZNA to achieve annual peak revenues exceeding $3 billion, supported by a significant addressable market and unmet patient needs [34] Other Important Information - The company reported non-GAAP R&D expenses of $6.1 million for Q4 2023, down from $14.3 million in Q4 2022, while SG&A expenses increased to $39.7 million from $25.7 million in the same period [40][58] - The company has access to a total of $160 million via its debt facility, providing a solid financial position to support its launch and development strategies [41] Q&A Session Summary Question: What is the company's comfort level with the consensus revenue estimates? - Management indicated that they expect normalized gross-to-net (GTN) dynamics to be between 50% and 65% [15][16] Question: Can you discuss the reasons for prescriptions not being filled? - Management noted that early on, some prescriptions were sent to long-established retail pharmacies, leading to a portion of VOQUEZNA prescriptions not being filled [54] Question: How does the company view the uptake of VOQUEZNA across different regions? - Management reported that they are seeing similar upticks in demand across the U.S., with positive feedback from physicians [69] Question: What is the expected trend for the split between BlinkRx and retail prescriptions? - Management expects the utilization of BlinkRx to grow over time, with a shift towards retail as more payer access is secured [88][91] Question: How is the company planning to approach the Eosinophilic Esophagitis Phase II trial? - The company intends to target a first-line treatment population, focusing on broader segments in the Phase II study [92]

Exhibit 99.1 Phathom Pharmaceuticals Reports Fourth Quarter and Full Year 2023 Financial Results and Provides Business Update FLORHAM PARK, N.J., March 7, 2024 — Phathom Pharmaceuticals, Inc. (Nasdaq: PHAT), a biopharmaceutical company focused on developing and commercializing novel treatments for gastrointestinal diseases, today reported financial results for the fourth quarter and full year ended December 31, 2023, and provided recent business highlights. "Last year was transformative for Phathom, with ke ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2023 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) (State or other jurisdiction of incorpora ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (State or other jurisdiction of incorporation or organization) Delaware 82-4151574 (I.R.S. Employer Identification No.) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2023 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 PHA ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2023 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) (State or other jurisdiction of incorporation ...

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, 2022 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 | | | 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 Incorporation or ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2022 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 juris ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2022 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 jurisdicti ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2022 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to . WASHINGTON, D.C. 20549 FORM 10-Q Commission File Number: 001-39094 PHATHOM PHARMACEUTICALS, INC. (Exact name of Registrant as specified in its charter) Delaware 82-4151574 (State or other jurisdict ...