Vaxcyte : Investor Presentation January 2023

Corporate Presentation

January 5, 2023

Forward-Looking Statements

This presentation contains forward-looking statements within the meaning of The Private Securities Litigation Reform Act of 1995. These statements include, but are not limited to, statements related to the potential benefits of Vaxcyte's vaccine candidates, including breadth of coverage and the ability to deliver a potentially best-in-class pneumococcal conjugate vaccine; demand for Vaxcyte's vaccine candidates; the timing of the initiation, progress and expected results of Vaxcyte's preclinical studies, clinical trials and research and development plans (including, the availability of data for the VAX-24 Phase 2 and Phase 3 studies and

related regulatory interactions; the submission of a VAX-24 infant IND application and initiation of such study; the design of the VAX-31 (formerly called VAX-XP) clinical program, the submission of such IND and the availability of topline data; the announcement of guidance for VAX-A1; the achievement of future funding milestones; the use and availability of funds from CARB-X; the growth and expansion of the pneumococcal vaccine market, and the potential for Vaxcyte's PCV franchise to have sustained leadership within such market; the potential conversion by the pneumococcal vaccine market to a prime-boost schedule; the market opportunity for Vaxcyte's vaccines; Vaxcyte's expectations regarding the potential benefits, spectrum coverage, regulatory pathway, adoption speed and immunogenicity of its vaccine candidates; VAX-31's advancement as a follow-on candidate to VAX-24; and other statements that are not historical fact. The

words "anticipate," "believe," "continue," "could," "designed," "estimate," "expect," "intend," "may," "plan," "potential," "predict," "project," "should," "target,"

"will," "would" and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words.

These forward-looking statements are based on Vaxcyte's current expectations and actual results and timing of events could differ materially from those anticipated in such forward-looking statements as a result of risks and uncertainties, including, without limitation, risks related to Vaxcyte's product development programs, including development timelines, success and timing of chemistry, manufacturing and controls and related manufacturing activities; potential delays or inability to obtain and maintain required regulatory approvals for its vaccine candidates; the risks and uncertainties inherent with preclinical and clinical development processes; the success, cost and timing of all development activities and clinical trials; sufficiency of cash and other funding to support Vaxcyte's development programs and other operating expenses; and the ongoing COVID-19 pandemic, which could materially and adversely affect Vaxcyte's business and operations. These and other risks are described more fully in Vaxcyte's filings with the Securities and Exchange Commission (SEC), including its Quarterly Report on Form 10-Q filed with the SEC on November 7, 2022 or in other documents Vaxcyte subsequently files with or furnishes to the SEC. Vaxcyte undertakes no duty or obligation to update any forward-looking statements contained in this release as a result of new information, future events or changes in its expectations.

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VAXCYTE MISSION STATEMENT

We are on a global mission to engineer high- fidelity vaccines that protect humankind from the consequences of bacterial diseases.

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Key Corporate Highlights

Clinical-Stage Vaccine Innovation Company - Led by Pneumococcal Conjugate Vaccine (PCV) Franchise

POTENTIAL BEST-IN-CLASS PCV FRANCHISE: VAX-24 & VAX-31

• Scalable platform enabling broader- spectrum carrier-sparingPCVs
• Lead candidate: VAX-24
• • Reported positive topline Phase 1/2 data results in adults
  • Potential best-in-class24-valent PCV designed to replace SOC in adults and children
  • Breakthough Therapy and Fast Track designations in adults
• Follow-oncandidate: VAX-31 (formerly VAX-XP)

	CELL-FREE PROTEIN		HIGHLY ATTRACTIVE
	SYNTHESIS PLATFORM		PCV MARKET
•	Leverages site-specific	•	Well-defined >$7B market
	conjugation to expose on-		segment poised for
	target T- and B-cell antigens		substantial growth
•	Enables carrier-sparing	•	Honors well-understood
	conjugates		PCV MOA
•	Permits production of	•	Leverages established
	"tough-to-make" antigens		surrogate immune
			endpoints and clinical
			pathways

• Spectrum of coverage is primary adoption driver

ROBUST DEVELOPMENT	ALIGNED CRITICAL
PIPELINE	RESOURCES
• Platform unlocks large	•	Strategic alignment with
market opportunities:		Lonza (manufacturing)
- VAX-A1: Novel Group A	•	Seasoned management
Strep conjugate vaccine		team, directors and advisors
- VAX-PG: Novel	• ~1.0B in cash, cash
periodontitis therapeutic		equivalents and investments
vaccine		as of 9/30/22 pro forma for
		Oct. 2022 follow-on
		offering(1)

• 31-valentPCV designed to provide coverage for ~95% of PD circulating in the U.S. adult population

1. Reflects cash, cash equivalents at September 30, 2022 of $366.2M and net proceeds from October follow-on offering of ~$650.7M.

SOC = Standard-of-Care.

PD = Pneumococcal Disease.

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Experienced Team with Track Record in Vaccines and Biopharma

Management Team

Grant Pickering, MBA

Andrew Guggenhime, MBA

Jim Wassil, MS, MBA

Mark Wiggins, MBA

CEO & Co-founder

President & CFO

EVP & COO

CBO

Jakub Simon, MD, MS

Jeff Fairman, PhD

Paul Sauer, MBA

Harp Dhaliwal, MBA

CMO

VP Research & Co-founder

SVP PD & Manufacturing

SVP Commercial Mfg & Supply Chain

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