1 Company Overview September 2015 NASDAQ: Exhibit 99.1

2 Forward Looking Statements Zogenix cautions you that statements included in this presentation that are not a description of historical facts are forward-looking statements. Words such as "believes," "plans," "expects," "will," "potential" and similar expressions are intended to identify forward-looking statements. These statements are based on the company's current beliefs and expectations. These forward-looking statements include statements regarding: the timing of the commencement and completion of clinical trials and regulatory submissions for ZX008 and RELDAY; the Company's cash position related to operating expenses and planned development activities; and delivery and dosing benefits of ZX008 and RELDAY and the potential to demonstrate that they have differentiated product profiles amongst currently marketed drug products. Actual results may differ from those set forth in this presentation due to the risk and uncertainties inherent in Zogenix's business, including, without limitation: difficulties or delays relating to the development, testing, manufacturing and marketing of any of Zogenix’s product candidates; the potential that earlier clinical trials may not be predictive of future results; Zogenix's reliance on third parties to conduct its clinical trials, enroll patients, manufacture its preclinical and clinical drug supplies and manufacture commercial supplies of its drug products, if approved; Zogenix's ability to fully comply with numerous federal, state and local laws and regulatory requirements that apply to its product development activities; Zogenix could spend its available financial resources faster than it currently expects and may be unable to raise additional capital if and when needed, on acceptable terms or at all; and other risks described in the company's filings with the Securities and Exchange Commission (SEC). You are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date hereof, and Zogenix undertakes no obligation to revise or update this release to reflect events or circumstances after the date hereof. All forward-looking statements are qualified in their entirety by this cautionary statement.

3 Developed, Commercialized and Monetized CHRONIC PAIN ACUTE MIGRAINES EPILEPSY (DRAVET SYNDROME) SCHIZOPHRENIA ONCE-MONTHLY ZX008 (low-dose fenfluramine) Late Stage Development Global Opportunities Products for the Treatment of CENTRAL NERVOUS SYSTEM (CNS) Disorders

4 The Zogenix Opportunity PROMISING PIPELINE of Differentiated CNS Compounds in Late-Stage Clinical Development FULLY FUNDED For Multiple Milestones Through 2017 for 2 Clinical Programs EXPERIENCED TEAM with Successful Track Record of Drug Development HIGHLY EFFICIENT Path to Commercialization and Profitability ORPHAN DRUG STRATEGY Focused on Solving Significant Treatment Gaps

5 • Worldwide Rights • Orphan Drug Designation in U.S. and E.U. • Expect to Commercialize Directly in U.S. and E.U. • Asia-Pacific Partnering Opportunity ZX008 Dravet Syndrome PHASE 3 START Q4 2015

6 Dravet Syndrome: A Catastrophic Illness Intractable, Severe Epilepsy Which Begins In Infancy • Estimated 16,000 - 29,000 Patients in the U.S. and E.U. 1 • Approximately 75 Specialty Treatment Centers in U.S. and similar in E.U. • Does not Effectively Respond to Traditional Epilepsy Medications • Cognitive, Developmental,                                                 Behavioral, and Motor Impairment                                 Correlated with >5 Seizures/Month 2 • Polypharmacy is Standard of Care But No Effective, Long-Term Treatment Exists 1. Calculated by patient incidence rates and population in US and in UK, Germany, Italy, Spain, France Bayat A et al; Epilepsia. 2015: 56(4):e36-9 (ISSN:1528-1167) The incidence of SCN1A-related Dravet syndrome in Denmark is 1:22,000: A population-based study from 2004 to 2009. Brunklaus, A. et al, Brain, 2012: 135; 2329-2336. Prognostic, clinical and demographic features in SCN1A mutation-positive Dravet syndrome Hurst, Daniel; Epilepsia. 31(4):397-400, 1990) Epidemiology of Severe Myoclonic Epilepsy of Infancy 2. Wolff M., Dravet C. Epilepsia, 2006; 47 Suppl 2:45-8. Severe myoclonic epilepsy of infants (Dravet syndrome): natural history and neuropsychological findings.

7 First Published Study of Fenfluramine Efficacy in Dravet Syndrome • Long-term open-label study of fenfluramine as an adjunctive anticonvulsant therapy • 12 Dravet syndrome patients, 11 with confirmatory genetic mutation • 70% of patients seizure-free at last assessment • Range of 1-19 years of seizure freedom Clinical data / IP                           licensed by Zogenix

8 This analysis includes 10 patients from the original cohort (5 years of follow- up) and 2 patients who began treatment  in 2011 (4 years of follow-up) Patients age range of 9 months to 13 years at treatment initiation Recent Multi-Year Follow-Up Analysis Further Supports Fenfluramine Efficacy in Dravet Syndrome • >80% of Patients Achieved  >75% Reduction in Seizure Frequency • 29 of 58 Patient-Treatment Years (50%) Were Seizure- Free • 3 out of 12 Patients Were Seizure-Free for All 5 Years • 5 out of 12 Patients Were Seizure-Free for 2-4 Years • No Clinically Significant Findings Related to Cardiotoxicity [Echocardiography] • Mild/Transient Side Effects: Loss of Appetite, Fatigue, Somnolence Categorical Response to Low-Dose (10mg – 20mg Daily) Fenfluramine Ceulemans, Berten, et al. Five-Year Follow-Up of Fenfluramine as Add-on Treatment in Dravet Syndrome. 11 th European Paediatric Neurology Society Congress, online poster presentation, May 2015.

9 Pre-Clinical Evidence of Fenfluramine Activity in an Established Model of Dravet Syndrome Zhang, Yifen, et al. PLOS May 12, 2015. Pharmacological Characterization of an Antisense Knockdown Zebrafish Model of Dravet Syndrome: Inhibition of Epileptic Seizures by the Serotonin Agonist Fenfluramine. • Zebrafish model of DS - antisense knockdown of scn1Lab – >80% of Dravet syndrome patients test positive for SCN1A gene mutations – Mutant, in contrast to wild type, zebrafish display hyperactivity, convulsive seizure-like behavior, loss of posture, repetitive jerking and a myoclonic seizure-like pattern • Demonstrated  the ability of fenfluramine to significantly reduce locomotion and  to eliminate epileptiform EEG activity • These data support the clinical results obtained in the Belgium cohort of patients Wildtype scn1Lab Mutant

10 History of Therapeutic Use of Fenfluramine • Off-Label Combination Use with Phentermine in 1980s/1990s, Often At Higher than Approved Doses • Approved Dosage: 60-120mg Daily – Substantially Higher than ZX008 dose in Dravet syndrome treatment • Fenfluramine Withdrawn Worldwide in late 90’s/early 2000’s Due to Heart Valve Problems in Obese Adults • >40 Studies Published Evaluating Fenfluramine > 400 Children • Focus on Treating Autism, ADHD • No CV Side Effects Reported Fenfluramine Approved Use in Adult Obesity Approved Use in Adult Obesity Experimental Use in Pediatric Neurobehavioral Conditions Experimental Use in Pediatric Neurobehavioral Conditions

11 Established Pathway to Phase 3 Development and Regulatory Submissions Summary of Correspondence with FDA and European Agencies • Recognition That Benefit/Risk in Dravet Syndrome Is Different to Use of Fenfluramine as an Appetite Suppressant • Confirmed Path to IND / CTA Submissions to Initiate Phase 3 Efficacy Trials – IND submitted at end of August 2015 – CTA to be submitted through Voluntary Harmonization Procedure – FDA requires establishment of cardiovascular monitoring procedures prior to study initiation • 505(b)(2) Pathway in U.S. Confirmed • Encouraged to Seek Fast Track Designation in U.S. Once IND is Active • Orphan Drug Designation Granted • Post-Approval REMS / Risk Management Plan Will be Required

12 ZX008 Summary of Phase 3 Study Design 8 WEEKS BASELINE OBSERVATION 12 WEEKS TREATMENT Initial Screen Placebo Open Label Safety Study N = 105 Ages 2 – 18 ZX008 High dose ZX008 Low dose • Two identical studies, one U.S. and one multinational (mainly Europe) • Q4 2015 initiation of U.S. study • Primary endpoint: change in convulsive seizures from baseline

13 E.U. 57% Market Research: ZX008 Could be Used as First or Second Adjunct Therapy in Dravet Syndrome % of Neuros Who Would Use ZX008 as a 1 st or 2 nd Adjunct Therapy Source: BioStrategies Market Research, May 2015 U.S. 81% Neurologists… • Were Overwhelmingly Positive Regarding the Safety and Efficacy Profile of ZX008 • Consider 78% of Dravet Syndrome Patients to be Clinically Appropriate for ZX008 Treatment Polypharmacy is Standard of Care for Management of Epilepsy

14 Established Product Protection ORPHAN DRUG STATUS May Provide 10 Years of Market Exclusivity in E.U. and 7 Years in U.S. When Obtained in Japan, ODS Will Provide 10 Years Exclusivity PATENTS PENDING (1) Use of Fenfluramine in Dravet Syndrome and Elements of a Future REMS Program Ongoing Preclinical & Development Work Providing Additional IP Opportunities PRODUCT SPECIFIC REMS Will Include Patient Registry and Cardiac Monitoring Difficult to Circumvent and Expensive to Replicate (1) Method For the Treatment of Dravet Syndrome – (13/887,014), (EP 2014/058954), (14/447/253), (14/447/303), (14/447,369)

15 Proprietary  Subcutaneous Once-Monthly Antipsychotic • Highly Differentiated Profile • Worldwide Rights • Co-Development/Commercialization Opportunity Schizophrenia PHASE 3 READY Q1 2016

16 Market Overview of LAIs for Treatment of Schizophrenia • 2.4 Million Diagnosed Patients in the U.S. • Treatment Compliance Can Be Challenging • Treatment Paradigm Evolving Towards Earlier Use of LAIs LAIs for Schizophrenia LAIs for Schizophrenia PATIENTS PHYSICIANS Large, Growing $4 – 5B WW Market • Highly Concentrated U.S. Market • 11,000 Psychiatrists Prescribing LAI Antipsychotics Source: Credit Suisse Securities Research, Dec. 9, 2014

17 RELDAY Has a Differentiated LAI Profile • Designed to overcome complexities associated with other long acting injections – No oral supplementation / complicated loading dose regimens – Initiation dose identical to maintenance dose • Once-monthly dosing interval • Subcutaneous administration – Potential for improved safety and tolerability • Stable formulation without the need for reconstitution prior to use

18 Strong Physician Endorsement of Product Attributes Relative to Marketed LAIs Highest on Clinical and Product Merits Very Positive/Positive On Initial Reaction Source: BioStrategies Group, 2013, N=150 U.S. Physicians, 173 E.U. Physicians U.S. E.U. 69% 61% RELDAY INVEGA® SUSTENNA® Risperdal® CONSTA® Abilify Maintena™ Zyprexa® Relprevv™ 7 POINT SCALE 1 = “Worst”     |     7 = “Best” Average (U.S. and E.U.) 5.1 4.4 4.2 3.9 3.4

19 Development Progress to Date • Single-Dose Study Successfully Completed • Multi-Dose Study Initiated: Top-Line Results Q3 2015 • Issued and Pending Patents Through at Least 2034 • Formulation Technology also Amenable to Three-Monthly Dosing Interval for Future Development and Life-Cycle Management A Proven, Effective and Safe Molecule for the Treatment of Schizophrenia

20 2015 Q1 Q2 Q3 Q4 Focused on Execution in Late-Stage Development ZX008 Submit IND / CTAs Initiate U.S. Phase 3 Initiate EU Phase 3 (Q1 2016) Targeting Phase 3 Results Prepare for NDA/MAA Submission End of Phase 2 FDA Meeting Initiate Phase 3 with Partner Phase 1B Results Expected AES scientific presentations 2016 Initiated Phase 1B Trial Initiate Partnering Discussions

21 Financial Highlights Cash ( balance at 6-30-15 plus follow-on offering net proceeds) $169.4 M         Debt (1) (as of 6-30-15) $20.0 M Guidance for 2H-2015 R&D expenses G&A expenses $19 M – $22 M $14 M – $16 M Common Shares Outstanding (2) 24.6 million Fully Diluted Shares (3) 29.0 million (1) Excludes $7.0 million working capital advance from Endo International (2) Common shares outstanding include 5.5 million shares issues in August 2015 follow-on offering (3) Fully diluted shares include options to purchase 2.4 million shares and warrants to purchase 2.0 million shares with weighted average exercise prices of $18.96 and $21.47, respectively

22 NASDAQ: PROMISING PIPELINE FULLY FUNDED CLINICAL PROGRAMS EXPERIENCED, SUCCESSFUL  TEAM SIGNIFICANT NEAR-TERM MILESTONES HIGHLY EFFICIENT PATH TO COMMERCIALIZATION