Phathom Pharmaceuticals : Erosive GERD Approval – November 2023

US APPROVAL OF VOQUEZNA® IN EROSIVE GERD & H. pylori

November 2023

NASDAQ: PHAT

Safe harbor

This presentation contains forward-looking statements. All statements other than statements of historical facts contained in this presentation, including statements regarding our future results of operations and financial position, anticipated milestones, anticipated cash runway, expectations of generating stability data necessary to support the proposed shelf life of vonoprazan, business strategy, prospective products, product approvals, research and development costs, timing and likelihood of success, plans and objectives of management for future operations, and future results of current and anticipated products, are forward-looking statements.

In some cases, you can identify forward-looking statements by terms such as "may," "will," "should," "expect," "plan," "anticipate," "could," "intend," "target," "project," "contemplates," "believes," "estimates," "predicts," "potential" or "continue" or the negative of these terms or other similar expressions. These statements involve known and unknown risks, uncertainties and other important factors that may cause our actual results, performance or achievements to be materially different from any future results, performance or achievements expressed or implied by the forward- looking statements. These risks, uncertainties and other factors include, without limitation: our ability to launch and successfully commercialize approved products containing vonoprazan; our new drug application for non-erosive GERD may not be filed or approved by the FDA; our Phase 3 trial for as need dosing of vonoprazan for non-erosive GERD may not successfully be completed; the inherent risks of clinical development of vonoprazan; our dependence on third parties in connection with product manufacturing, research and preclinical and clinical testing; regulatory developments in the United States and foreign countries; unexpected adverse side effects or inadequate efficacy of vonoprazan that may limit its development, regulatory approval and/or commercialization, or may result in recalls or product liability claims; our ability to obtain and maintain intellectual property protection for vonoprazan; our ability to comply with our license agreement with Takeda; our ability to achieve and maintain adequate levels of coverage and reimbursement for vonoprazan; the availability of additional funds under our revenue interest financing agreement and term loan agreement; the sufficiency of our capital to fund our operations; and other risks described in our filings with the Securities and Exchange Commission (SEC), including our Annual Report on Form 10-K and any subsequent filings with the SEC. You are cautioned to place undue reliance on these forward-looking statements, which speak only as of the date hereof, and we undertake no obligation to revise or update this presentation to reflect events or circumstances after the date hereof. All forward-looking statements are qualified in their entirety by this cautionary statement, which is made under the safe harbor provisions of the Private Securities Litigation Reform Act of 1995.

This presentation also contains estimates and other statistical data made by independent parties and by us relating to market size and other data about our industry. This data involves a number of assumptions and limitations, and you are cautioned not to give undue weight to such estimates. In addition, projections, assumptions, and estimates of our future performance and the future performance of the markets in which we operate are necessarily subject to a high degree of uncertainty and risk.

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Today's Agenda

Introduction

• Terrie Curran, Chief Executive Officer

Erosive GERD & H. pylori Disease State & Label

• Terrie Curran, Chief Executive Officer

Commercial Strategy

• Martin Gilligan, Chief Commercial Officer

Question & Answer

• Terrie Curran, Chief Executive Officer
• Martin Gilligan, Chief Commercial Officer
• Azmi Nabulsi, Chief Operating Officer
• Molly Henderson, Chief Financial Officer

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VOQUEZNA® is the first ever innovative acid suppressant to demonstrate superiority compared to a PPI across multiple indications

1st PCAB entrant in US

Belonging to a novel class

of therapies called Potassium

Competitive Acid Blockers

3 successful Ph 3 programs

Registrational trials across three indications: H. pylori (HP), Erosive GERD, & Non-Erosive GERD

Phathom is excited to introduce VOQUEZNA to the US market

Building upon demonstrated success:

Approved in 10+ countries worldwide

Tens of millions of patients treated

• Blockbuster in Japan:
  #1 prescribed acid suppressant1

>20 million people treated annually for acid related disorders2

1 IQVIA MIDAS as of June 30, 2023, amongst all PPI and PCAB molecules

2	Published epidemiology studies in combination with company estimates based on its market research
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PCABs demonstrate mechanistic differences compared to PPIs

PPI:VOQUEZNA:

COVALENTLY BINDING PRODRUG

COMPETITIVE ENZYME INHIBITOR

Secretory

canaliculus

Secretory

canaliculus

Quiescent phase	Active phase after meal
Tubulovesicle	Proton pump (H+, K+ -ATPase)

Quiescent phase	Active phase after meal
	Tubulovesicle	Proton pump (H+, K+ -ATPase)

• Short plasma half-life
• Acid needed for activation but unstable in presence of acid
• Meal required to stimulate pumps

Slow onset of action

Limited potency

Limited duration of activity

• Long plasma half-life
• Stable in acid
• High accumulation in canaliculus
• Very slow dissociation rate

Rapid onset of action

Potent acid control

Durable 24-hr activity

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VOQUEZNA foundation is built on superior acid suppression to transform GERD management

VOQUEZNA US potential peak revenue opportunity >$3B*

Strategy to become the #1 prescribed acid suppressant

GERD Transformation

Superiority

Foundation

Displace

PPIs

Non-Erosive GERD - Symptom Relief

Daily	As Needed

Erosive GERD - Healing and Maintenance

HP - Eradication

VONO 103 - Rapid, Potent, Durable Acid Suppression

Growth potential

6 * Company estimates based on its market research

VOQUEZNA® Triple Pak® & VOQUEZNA® Dual Pak® are indicated for the treatment of Helicobacter pylori (H. pylori) infection in adults

Product expected to be available in December

H. pylori (HP) Disease State

Eradication rates have fallen to<80% in the US1

Increasing antibiotic resistance & complex regimens driving treatment failure

Antibiotic potency increases at higher pH

With superiority claims versus a PPI-based triple therapy in the label,

VOQUEZNA Triple Pak and Dual Pak offer a new approach to possible first line eradication

1 Based on several retrospective queries of electronic records: Alsamman MA et al. Dig Dis Sci. 2019;64:2893-2898, Tariq H et al. Clin Exp Gastroenterol. 2020;13:25-33, and Argueta EA et al. Gastroenterology. 7 2021;160:2181-2183

VOQUEZNA is now the FIRST AND ONLY FDA APPROVED PCAB in the US

Product expected to be available in December

VOQUEZNA is indicated for the

healing and maintenance of healing of all grades of erosive esophagitis and relief of heartburn in adults.

VOQUEZNA is a novel, first-in-class,potassium-competitive acid blocker (PCAB) and the first innovative

acid suppressant from a new drug class approved in the US in over 30 years.

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The US Erosive GERD market is primed for a new treatment option

Prescription	Large	High	Frequent
Based	Population	Dissatisfaction	Switching

~85% of the total	~7M adults in the	Less than 50%	~35% of patients
PPI volume-based	US are diagnosed		of patients are	treated with a
market is driven by	with Erosive GERD		satisfied with	prescription PPI
	Rx vs. OTC1	and treated with a	current treatment4	switch to a
			prescription				different PPI after
	~110M PPI TRx	annually3	~60% of patients	~3 months5
	are written and			believe better
	filled annually			symptom control
	(all indications)2		can be achieved4

1 IQVIA NPA & Consumer Health Care Data Q1-3 2022; 2 IQVIA Xponent retail & mail-order Rx data (2022); 3 Published epidemiology studies in combination with company estimates based on its market research

4 Vaezi MF, Brunton S, Mark Fendrick A, et al. Patient journey in erosive esophagitis: real-world perspectives from US physicians and patients. BMJ Open Gastroenterology 2022;9:e000941. doi: 10.1136/bmjgast-2022-000941

5	Phathom data on file, diagnosed Erosive GERD patients between Jan. 2016 - Feb. 2022 (n=265,717)
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Overview of VOQUEZNA prescribing information

Products	VOQUEZNA 10mg (30-ct) & VOQUEZNA 20mg (30-ct)
	VOQUEZNA is a potassium-competitive acid blocker indicated for the:
	• Healing of all grades of erosive esophagitis and relief of heartburn associated with erosive esophagitis in adults.
Indications &	• Maintenance of healing of all grades of erosive esophagitis and relief of heartburn associated with erosive
esophagitis in adults.
Usage
• In combination with amoxicillin and clarithromycin for the treatment of Helicobacter pylori (H. pylori) infection in
	adults.
	• In combination with amoxicillin for the treatment of H. pylori infection in adults.
	Recommended Dosage:
	• Healing of Erosive Esophagitis: 20 mg once daily for 8 weeks.
	• Maintenance of Healed Erosive Esophagitis: 10 mg once daily for up to 6 months.
	• Treatment of H. pylori Infection: see full prescribing information.
Dosage and	• See also full prescribing information for the recommended dosage by indication for patients with renal or
Administration	hepatic impairment.
	Administration Instructions:
	• Take with or without food.
	• Swallow whole; do not chew or crush.
	Most common adverse reactions in VOQUEZNA-treated patients are:
	• Healing of Erosive Esophagitis(≥2%): gastritis, diarrhea, abdominal distension, abdominal pain, and nausea.
Adverse	• Maintenance of Healed Erosive Esophagitis(≥3%): gastritis, abdominal pain, dyspepsia, hypertension, and
Reactions	urinary tract infection.
	• Treatment of H. pylori Infection(≥2%): diarrhea, dysgeusia, vulvovaginal candidiasis, abdominal pain,
	headache, hypertension, and nasopharyngitis.

For full prescribing and safety information, please visit VOQUEZNA.com

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