Corporate PresentationNYSE American: PFNX

Safe Harbor StatementPfenex

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 future potential of Pfenex's product candidates, including future plans to advance, develop, manufacture and commercialize its product candidates; potential market opportunities for PF582, PF708, PF529, PF690, Px563L/RPA563 and Pfenex’s other product candidates; Pfenex's expectation to receive data from the PF708 clinical program in the first half of 2018 and its expectation to submit an NDA in the third quarter of 2018; the expected patent expiration timelines for Lucentis, Forteo, and other branded reference drugs; developments and projections relating to competitors and the industry, including support of the US administration for development of medical countermeasures; expected milestones for Px563L/RPA563, including the timing of the Phase 2 study initiation, additional options triggered by the U.S. Government to fund the progression of manufacturing, non-clinical development, and preparatory activities for the Phase 2 trial; the potential of Pfenex’s anthrax vaccine candidates to fulfill the strategic national stockpile; expectations with regard to future milestone and royalty payments from Pfenex’s collaboration with Jazz Pharmaceuticals; expectations with respect to Pfenex’s ability to receive future payments under its government contracts; Pfenex’s expectations regarding the use of abbreviated regulatory pathways for the approval of its product candidates, including use of the 505(b)(2) regulatory pathway for PF708 and the 351(k) pathway for PF529; Pfenex's expectations regarding the timing and advancement of clinical trials and the types of future clinical trials for its product candidates, including PF708 and Px563L/RPA563; and Pfenex's expectation for potential strategic partnership opportunities for advancement of PF582, PF529, and its other product candidates. 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 PF708, Px563L/RPA563, and our other product candidates; our reliance on our collaboration partner’s performance over which we do not have control; failure to achieve favorable results in later clinical trials for PF708, Px563L/RPA563, 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 PF708, Px563L, or our other product candidates due to the existence of intellectual property protection owned or controlled by a third party and directed to PF708, Px563L/RPA563, or our other product candidates; PF708, Px563L/RPA563 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, 2017 press release announcing results for the quarter ended September 30, 2017. You should read our Annual Report on Form 10-K for the year ended December 31, 2016, our Quarterly Report on Form 10-Q for the quarter ended September 30, 2017 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. 2

3

► Pfenex Inc. is a clinical-stage biotechnology company developing complex therapeutic proteins. Using the patented Pfenex Expression Technology® platform, the company has created an advanced pipeline of therapeutic equivalents, vaccines, biologics and biosimilars

► Extensive competencies from early R&D to regulatory filing and partnership management

► San Diego-based, listed on NYSE American: PFNX

OverviewPfenex

4

Proven success developing complex therapeutic proteins with Pfenex Expression Technology™ platform

Proven Platform

Near-term Catalysts

Strong Management

PF708 top-line immunogenicity data readout expected 1H18, anticipated NDA submission in 3Q18; Development contract with the US Government (HHS via BARDA) towards Phase 2 study initiation expected for our anthrax vaccine candidate

Recently appointed Evert (Eef) Schimmelpennink as CEO; added Jason Grenfell-Gardner (Chairman) and Sigurdur (Siggi) Olafsson to Board of Directors

PfenexCompany Overview

Attractive Portfolio

Differentiated portfolio of therapeutic equivalents, vaccines, biologics and biosimilars

Scalable Technology

Opportunity to select additional partnered and wholly owned products for development up to various stages in cycle

5

Evert (Eef) Schimmelpennink (Aug 2017)CEO, President and Secretary

Patrick K. LucyChief Business Officer

Hubert ChenChief Medical & Scientific Officer

Sen

ior

Man

agem

ent

Bo

ard

of

Dir

ecto

rs

PfenexNew and Established Leadership Aligned to Drive Growth

Jason Grenfell-GardnerMay 2017 John TaylorDennis Fenton Philip SchneiderRobin Campbell

Mayda MercadoVice President, Quality

Sigurdur OlafssonMay 2017

Platform and Products in Development

7

1 2 3Advanced Strain Engineering Accelerated Development Robust Analytics

Our proprietary protein production platform, based on Pseudomonas fluorescens, allows for rapid, high quality production and analysis of difficult-to-produce proteins.

PfenexExpression Technology Platform

► Proven success with Pfenex Expression Technology™

► Worked with 60+ biopharmaceutical companies with our protein expression platform

► 80% success rate where other previously-used systems failed

► Therapeutic equivalents, vaccines, biologics and biosimilars

8

Products in DevelopmentPipeline Highlights

PF7081

Teriparatide (Forteo®)

PF582Ranibizumab (Lucentis®)

PF529Pegfilgrastim (Neulasta®)

PF690Pegaspargase (Oncaspar®)

Jazz PartnershipMultiple Hematology Products

PRECLINICAL ANALYTICAL SIMILARITY

US FDA BIOSIMILARINITIAL ADVISORY

MEETING

COMPARATIVE CLINICAL STUDY

INITIAL | CONFIRMATORY

REGULATORYSUBMISSION

PRECLINICAL PHASE 1 PHASE 2

PX563LAdjuvanted Anthrax Vaccine

EXISTING USGTHIRD-PARTY

ANTHRAX VACCINE

CONTRACT5 YEARS - $911MM3

RPA563Non-Adjuvanted Anthrax Vaccine

FULLY FUNDED BYUS GOVERNMENT

POTENTIAL PROCUREMENT

$1.5B

REFERENCE DRUG 2016

GLOBAL SALES2

$3.2B

$4.6B

$0.2B

PF708 (teriparatide [rDNA] injection

9

► Forteo® (teriparatide) rDNA protein and pen combination product

► Indicated for treatment of high fracture risk osteoporosis

► 2016 global sales of $1.5B of reference drug

► Pfenex has achieved:

► high titer protein production

► low cost of goods

► Functionally equivalent pen device

► Demonstrated bioequivalence in healthy subjects

Pla

sma

Teri

par

atid

e (p

g/m

L)

Products in DevelopmentPF708: Therapeutic Equivalent Candidate to Forteo®

Mean ± Standard DeviationTime (hr)

Bioequivalence results in healthy subjects

10

► Ongoing osteoporosis study

► Fully enrolled with 181 subjects

► Interim results indicate comparable PK profiles between PF708 and Forteo®

► Complements prior bioequivalence results in healthy subjects

► Key Upcoming Expected Milestones:

► Primary endpoint of immunogenicity anticipated in first half of 2018

► 505(b)(2) NDA filing expected second half 2018

► Latest expiry of Orange Book-listed teriparatide method of treatment, formulation and/or API patent expected in 2019 in US

Products in DevelopmentPF708: Therapeutic Equivalent Candidate to Forteo®

Mean ± Standard Deviation

Comparable PK results in osteoporosis patients

Osteoporosis study design

11

► Awarded a BARDA contract in August 2015 of up to $143.5MM to fund advanced development

► Anthrax recombinant Protective Antigen (rPA) vaccine candidates:► Demonstrated long term stability data from

toxicology lot showing the maintenance of high purity at 5°C at 40 months.

► Phase 1a Day 70 analysis demonstrated that Px563L and RPA563 were well-tolerated and afforded immunogenicity protection with fewer doses than the currently licensed product

► US administration has demonstrated strong support for development of medical countermeasures (MCMs)

► Current sole sourced contract is valued at close to $1B for a 5 year supply6

Products in DevelopmentPx563L/RPA563: Next Gen Anthrax Vaccine Candidates

0.03

0.3

3

30

0 14 28 42 56 70

PBO

10 mcg

50 mcg

80 mcg

0.03

0.3

3

30

0 14 28 42 56 70

PBO

10 mcg

50 mcg

80 mcg

Toxin Neutralizing Antibody NF50 Results

To

xin

Neu

tral

izin

g A

ntib

od

y N

F50

(G

eom

etri

c M

ean

Tit

er ±

95%

Co

nfid

ence

Inte

rval

s)

Time (Day)

Time (Day)

RPA563

Px563L

REGULATORY THRESHOLDNF50 ≥ 0.56

12

► In addition to the amounts originally granted, BARDA exercised two options in January 2017, allowing for continued development

► Key Upcoming Expected Milestones:► Potential triggering of options in our

development contract which will fund the progression of manufacturing, nonclinical development, and preparatory activities for the Phase 2 trial

► The Phase 2 study could initiate late 2018, provided the program continues to successfully advance with the support of BARDA as described above

► Potential procurement contract if within 10 years of FDA approval

► We believe Pfenex is the only company funded by the US Dept. of Health and Human Services via BARDA developing a next generation rPA based anthrax vaccine that is able to potentially fulfill the needs of the Strategic National Stockpile (SNS)

Products in DevelopmentPx563L/RPA563: Next Gen Anthrax Vaccine Candidates

13

► License and option agreement signed in July 2016 granting Jazz Pharmaceuticals worldwide rights to develop and commercialize multiple early-stage hematology product candidates

► Collaboration details:

► Up to $181 MM in 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

► Process development milestone achieved in Q3 2017

► Jazz obtains exclusive option to PF690, Pfenex’s pegaspargase biosimilar candidate to Oncaspar®

Products in DevelopmentJazz Pharmaceuticals/Pfenex Collaboration

14

► Global Lucentis® market was $3.2 billion in 20167

► Latest known composition of matter expected patent expiry: USA 2020; EU 20228

► Phase 1/2 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

► Pfenex considering strategic partnership opportunities for advancement to maximize value

Pipeline ProductsPF582: Biosimilar to Lucentis®

Bes

t C

orr

ecte

d V

isua

l Acu

ity

Sco

re ±

SD

PF582 Lucentis

15

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

► Neulasta global sales in 2016: $4.6 billion9

► US FDA feedback for PF529 was received in Q4 2016 supporting the feasibility of development under the 351(k) biosimilar pathway

► Pfenex considering strategic partnership opportunities for advancement to maximize value

Pipeline ProductsPF529: Biosimilar Candidate to Neulasta®

Q216 Q316 Q416 1H17 2H17 1H18 2H18 2019 2020

16

Programs in our pipeline include five programs in clinical development, including one therapeutic equivalent, two vaccine candidates and two biosimilar candidates.

PfenexOverview & Investment Highlights

JAZZ PHARMACEUTICALS

PARTNERSHIP ANNOUNCED

PF708 - teriparatide Px563L – Anthrax vaccine PF582 - ranibizumab PF529 - pegfilgrastim

PF708:POSITIVE TOPLINE STUDY RESULTS ANNOUNCED

PF708:PIVOTAL STUDY INITIATED

PF708:IMMUNOGENICITY STUDY RESULTS ANTICIPATED

PF708:POTENTIAL NDAFILING

PF708:INTERIM PK STUDY RESULTSANNOUNCED

PF708:EXPECTED FORTEO® PATENT EXPIRY (WITH RESPECT TO API, MOT AND/OR FORMULATION PATENTS IN US)

PX563L:POSITIVE PHASE 1 DAY 70 ANALYSISCOMPLETED

PX563L:CONSULTATION WITH BARDA

PX563L:POTENTIAL

OPTION TRIGGERED FOR

CLINICAL MANUFACTURING

PF582:PHASE 1/2 COMPLETED

PF582:EXPECTED LUCENTIS®PATENT EXPIRY IN US

PF529:REGULATORY FEEDBACKRECEIVED

PX563L:POTENTIAL

PHASE 2 STUDYINITIATION

17

Proven Platform

Near-term Catalysts

Strong Management

Pfenex

Attractive Portfolio

Scalable Technology

INNOVATIVE SOLUTIONS FOR GLOBAL HEALTH

© 2017 Pfenex Inc. All rights reserved.

19

1. Being developed via the 505(b)(2) pathway in the United States2 Based on publicly available 2016 sales data for the third party branded pharmaceutical company3 https://www.sec.gov/Archives/edgar/data/1367644/000136764416000084/form8kearningsq3q2016.htm4 Eli Lilly Annual Report 2016, Page 245 Forteo® teriparatide patent, U.S. patent no. 7,351,414 B26 https://www.sec.gov/Archives/edgar/data/1367644/000136764416000084/form8kearningsq3q2016.htm7 2016 Roche Annual report8 GaBI Online, http://www.gabionline.net/Biosimilars/General/Biosimilars-of-ranibizumab9 Amgen Annual Report 2016

PfenexReferences