Corporate Presentation January 2017

• This presentation (the “Presentation”) includes forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, which are based on current expectations, estimates and projections based on information currently available to management. These forward-looking statements include, among others, statements regarding the timing of the initiation and completion of our anticipated clinical trials and studies for PF708, PF529 and our other product candidates; expectations with regard to future milestone and royalty payments from our collaboration with Jazz Pharmaceuticals; potential market opportunities for PF582, PF708, PF529 and our other product candidates; potential market size and growth potential of the biosimilars and biologics markets; developments and projections relating to competitors and the industry, including the rate and degree of market acceptance of biosimilars by stakeholders and physicians; the potential outcomes and timing of our discussions with BARDA with respect to Px563L; the expected patent expiration timelines for Lucentis, Forteo, and other branded reference drugs; the potential outcomes and timing of our discussions with governmental regulatory agencies for PF529 and our other product candidates; our anticipated commercialization strategy, including the timing of our commercial process lockdown for Px563L; our expectations regarding the use of abbreviated regulatory pathways for the approval of our product candidates, including our use of the 505(b)(2) regulatory pathway for PF708;expectations with regard to government expenditures for vaccine procurement, including our potential to obtain a government procurement contract for Px563L if within ten years of FDA approval; and the timing of our anticipated technology transfer of Product 1 under our collaboration with Jazz Pharmaceuticals. Forward-looking statements are typically identified by words like “believe,” “anticipate,” “could,” “should,” “estimate,” “expect,” “intend,” “plan,” “project,” “will,” “forecast,” “budget,” “pro forma,” and similar terms. Factors that could cause the Company’s results and expectations to differ materially from those expressed in forward-looking statements include, without limitation, our need for additional funds to support our operations; our success being dependent on PF582, PF708, and our other product candidates; our reliance on our collaboration partners’ performance over which we do not have control; failure to achieve favorable results in later clinical trials for PF582, PF708, or our other product candidates or receive regulatory approval; delays in our clinical trials or in enrollment of patients in our clinical trials; failure to market PF582, PF708, or our other product candidates due to the existence of intellectual property protection owned or controlled by a third party and directed to PF582, PF708, or our other product candidates; PF582, PF708, and our other product candidates may cause serious adverse side effects or have properties that delay or prevent regulatory approval or limit their commercial profile; if approved, risks associated with market acceptance, including pricing and reimbursement; our ability to enforce our intellectual property rights; adverse market conditions; and changes to laws and government regulations involving the labelling, approval process, funding and other matters affecting biosimilars, therapeutic equivalents to branded products and vaccines. Forward-looking statements represent our management’s beliefs and assumptions only as of our November 9, 2016 press release announcing results for the quarter ended September 30, 2016. You should read our Annual Report on Form 10-K for the year ended December 31, 2015, our Quarterly Report on Form 10-Q for the quarter ended September 30, 2016, and our subsequent reports filed with the SEC, including the Risk Factors set forth therein, completely and with the understanding that our actual future results may be materially different from what we expect. Except as required by law, we assume no obligation to update these forward-looking statements publicly, or to update the reasons why actual results could differ materially from those anticipated in the forward-looking statements, even if new information becomes available in the future.

Safe Harbor Statement

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Programs in development pipeline include four programs in clinical development including three biosimilars and one vaccine

Corporate Overview &

Investment Highlights

Q3 2015 Q4 2015 Q1 2016 Q2 2016 Q3 2016 Q4 2016 2017 2018 2019 2020

PF708: Bioequivalencestudy initiated

Px563L:US Government development contract awarded

PF708: Positive topline study results reported

Jazz Pharmaceuticals partnership announced

PF582: Phase 1b/2a completed

Px563L: Positive Phase 1 Day 70analysis completed

PF708: Planned initiation of pivotal study

PF529: Regulatory feedback anticipated

PF708: ExpectedForteo® patent expiry

PF582: ExpectedLucentis® patent expiry

Px563L: Plannedconsultation with BARDA

PF708

Px563L

PF582

PF529

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Pfenex Pipeline

PRECLINICAL/ BIOANALYTICAL CHARACTERIZATION

COMPARATIVE CLINICAL STUDY

$11

Billion

PF688Certolizumab

pegol

biosimilar

(Cimzia®)

$1.2B*

PF529Pegfilgrastim

biosimilar

(Neulasta®)

$4.7B*

PF708

Teriparatide

therapeutic

equivalent to

(Forteo®)

$1.4B*

PF690Pegaspargase

biosimilar

(Oncaspar®)

$121MM**

PF582Ranibizumab

biosimilar

(Lucentis®)

$3.6B*

TOTAL APPROX. SALES OF BRANDED REFERENCE

DRUGS (2015)

HemOnc

Products

$3.9

Billion

PF694Peginterferon

alpha-2a

biosimilar

(Pegasys®)

$403MM**

PF444Human Growth

Hormone

biosimilar

$3.5B***

PRE-CLINICAL PHASE 1 PHASE 2

*Based on publicly available 2015 sales data for the branded pharmaceutical company.

**Approximate 2015 global branded sales of third-party reference drug per IMS data accessed May 4, 2016.

*** Approximate 2015 aggregate global branded sales of third-party growth hormone products per IMS data accessed May 4, 2016.

Px563LSDl rPA based Anthrax

Vaccine 2nd

Generation

Px563LrPA based

Anthrax Vaccine

RPA563rPA based

Anthrax Vaccine

Fully funded by US Government

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• Our unique Expression Technology allows for rapid, high quality production of therapeutics and vaccines and a revolutionary advancement in clinical technology.

Pfenex Expression Technology

GOAL:HIGH QUALITY, HIGH TITER

TRADITIONAL: TRIAL AND ERROR

PRIMARY STRUCTUREAmino acids are the primary structures of a

protein, linked together by peptide bonds,

which form a polypeptide. Biosimilars are first

compared at the polypeptide level.

SECONDARY STRUCTUREPolypeptides are then coiled into a

helix - this is the secondary

structure that is compared for

biosimilarity.

TERTIARY STRUCTUREThese helixes of polypeptides then

fold together in a specific manner. This

resulting tertiary structure is then

considered for biosimilarity.

QUATERNARY STRUCTUREThese polypeptide folds interact to

form a functional protein. This is the

quaternary structure considered for

biosimilarity.

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Biosimilars Market Landscape

Learning from the EU:

US Biosimilars Gaining Momentum EU Biosimilar Product Reviews as of October 2016

The 351(k) pathway enables the expedited development of biosimilar products by minimizing the clinical testing requirement2 Current US Biosimilar Pipeline Programs by Year3

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51 Marketing Authorization Applications (MAA)

submitted

17 MAAs under review34 MAAs reviewed

22 approved

7 accelerated Biologics License Applications (aBLA)

submitted

66 programs in the Biosimilar Biologic Product

Development (BPD) program

7 aBLA’s reviewed

4 approved

US Biosimilar Product Reviews as of October 2016

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Biosimilars Expand Patient Access to Therapy

Filgrastim Uptake in the EU

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• NOR-SWITCH Study: Physicians more comfortable switching patients to a biosimilar

• United Healthcare, Express Scripts, CVS Health have excluded Neupogen from their formulary in favor of its biosimilar Zarxio. Healthcare systems establishing biosimilars only tiers. (OPERS)

Stakeholders are Responding

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Our Products in Development

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• Latest known composition of matter patent expiry: USA 2020; EU 2022• Phase 1b/2a first-in-human study completed:

• Met primary objective of demonstrating similar safety and tolerability between PF582 and Lucentis• Demonstrated consistent pharmacological activity between PF582 and Lucentis.

• Evaluating strategic options

PF582: Biosimilar to Lucentis®

Figure 1: No significant differences in best corrected visual acuity (BCVA)

Figure 2: Comparable decreases in central retinal thickness

Figure 3: Comparable immunogenicity (anti-drug antibody formation)

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• Forteo® (teriparatide) indicated for treatment of high fracture risk osteoporosis• Reference product produced via E. coli• Forteo global sales in 2015: $1.4 billion5

• Expected section 505(b)(2) regulatory approval pathway for PF708• Latest expiry of Orange Book-listed teriparatide method of treatment, formulation and/or API patent expected in 2019.

• Pfenex has achieved high titer protein production; low cost of goods• Completed bioequivalence in healthy subjects that met endpoints • Pivotal immunogenicity/pharmacokinetic study in subjects with osteoporosis expected to begin by end of 2016

PF708: Therapeutic Equivalent

Candidate to Forteo®

•

Study Design

Results

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• Neulasta® (pegfilgrastim) is indicated for the prevention of febrile neutropenia in patients receiving cytotoxic chemotherapy

• Neulasta ® global sales in 2015: $4.7 billion6

• Anticipate regulatory feedback by end of 2016

PF529: Potential Biosimilar

to Neulasta ®

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• In August 2015 awarded a BARDA contract of up to $143.5MM to fund advanced development

• Anthrax recombinant Protective Antigen (rPA) vaccine candidates:• Phase 1a Day 70 analysis demonstrated that

Px563L was well-tolerated and conferred potentially superior protection after only 2 doses

• Potential procurement contract if within 10 years of FDA approval

Px563L: Next Generation

Anthrax Vaccine CandidateFigure 1: Toxin Neutralizing Antibody NF50 Results

Table 1: Positive Day 70 Immunogenicity Results for Px563L

• Regulatory Threshold For Post Exposure Prophylaxis Indication:• For the percentage of subjects with TNA NF50 value ≥0.56, the

lower limit of the 95% confidence interval should be ≥40%.

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• Agreement signed in July 2016

• License and option agreement granting Jazz Pharmaceuticals worldwide rights to develop and commercialize multiple early stage hematology product candidates

• Partnership details:

• $181 MM in combined upfront and potential milestone payments including up to $41 MM non-sales related; tiered royalties on net sales

• Collaboration governed by Joint Development Committee with equal representation from each company

• Jazz obtains exclusive option to PF690, Pfenex’s Pegaspargase biosimilar candidate to Oncaspar®

Jazz Pharmaceuticals/Pfenex Collaboration

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Corporate Overview &

Investment Highlights

Px563L: Anticipated consultation with BARDA

Q3 2015 Q4 2015 Q1 2016 Q2 2016 Q3 2016 Q4 2016 2017 2018 2019 2020

PF708: Bioequivalencestudy initiated

Px563L:US Government development contract awarded

PF708: Positive topline study results reported

Jazz Pharmaceuticals partnership announced

PF582: Phase 1a/2b completed

Px563L: Positive Phase 1 Day 70analysis completed

PF708: Planned initiation of pivotal study

PF529: Regulatory feedback anticipated

PF708: Expected Forteo® patent expiry

PF582: Expected Lucentis® patent expiry

2017 Catalysts• PF708 – Expected Completion of Comparative

Clinical Study

• PF529 – Planned Initiation of Comparative Clinical Study

• Jazz Collaboration – Anticipated Technology Transfer of Product 1

• Px563L – Anticipated Commercial Process Lockdown

• PF582 – Planned Initiation of Clinical Comparative Study

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Appendix

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Senior Management

Patrick K. LucyInterim CEOChief Business Officer

Paul WagnerPh.D., CFAChief Financial Officer

Patricia LadyM.B.A., CPAChief Accounting Officer

Hubert ChenM.D.Chief Medical Officer

Steven S. SandovalChief of Manufacturing and Operations

Henry TalbotPh.D.Vice President, Operations

Mitchell GonzalezPMPVice President, Manufacturing & Process Sciences

Mayda MercadoVice President of Global Quality

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• William R. Rohn (Chairman)William R. Rohn joined the board of directors as the chairman in connection with Pfenex’s initial public offering in July 2014. Most recently, Mr. Rohn served as Chief Operating Officer of Biogen Idec, the successor company to IDEC Pharmaceuticals, a biotechnology company, from 2003 until 2005.

• Robin D. Campbell, Ph.D.Dr. Robin D. Campbell joined the board of directors in September 2014. He has over 25 years of experience in pharmaceutical and biotechnology sales, marketing, product development and general management in both the U.S. and in international markets. Currently he serves as Chairman of the Board of Aptitude Medical Systems, an early stage company creating high performance aptamers for research, diagnostic and therapeutic use.

• Phillip M. Schneider, M.B.A.Phillip M. Schneider joined the board of directors in connection with Pfenex’s initial public offering in July 2014. Most recently, Mr. Schneider held various positions with IDEC Pharmaceuticals Corporation, a biopharmaceutical company, from 1987 to 2003, including: Senior Vice President and Chief Financial Officer from 1997 to 2003; and Director of Finance and Administration from 1992 to 1997.

• John Taylor, J.D.John Taylor joined the board of directors in April 2015. He is a Principal of Compliance and Regulatory Affairs at Greenleaf Health LLC., and has over 24 years of experience working on food and drug related issues at the U.S. Food and Drug Administration (FDA)and in private industry.

• Dennis Fenton, Ph.D.Dr. Dennis Fenton joined the board of directors in September 2015, deepening the manufacturing and product development expertise of our company. Dr. Fenton, an industry pioneer, has over three decades of experience in the biotechnology industry. Dr. Fenton retired after a lengthy and distinguished career with Amgen, where he held a variety of notable roles, including Executive Vice President, Operations.

Board of Directors

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The Pfenex Toolbox

Elements combined to generate >100 rapid cloning, off the shelf, expression vectors covered by our numerous issued/allowed patents**As of March 7, 2016

Our patent protected ability to enable rapid strain engineering for optimal protein production accelerates proof of concept, product development and long-term cost of goods advantage.

Cell Model

Our model enables 5,400,00+ opportunities for strain development.

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• Biosimilars in the US: Progress and Promise DIA Biosimilars 2016 John Jenkins, M.D. Director Office of New Drugs Center for Drug Evaluation and Research October 27, 2016

• BCC Research. “Biologic Therapeutic Drugs: Technologies and Global Markets,” Jan. 2015, p. 2.• IMS Health, “Shaping the biosimilars opportunity: A global perspective on the evolving biosimilars landscape.” Dec. 2011, p. 6. • Bayer Annual Report 2015, p. 156.• Eli Lilly Annual Report 2015, p. 40.• Amgen Annual Report 2015, p. 44• Medicines for Europe, “Biosimilar Medicines: Did You Know?” accessed Apr. 2016.• Generics and Biosimilars Initiative Journal, “Saving Money in the European Healthcare Systems with Biosimilars,” 2012, p. 124.

References

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