NASDAQ: ZGNX. Company Presentation. October 2017

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NASDAQ: ZGNX Company Presentation October 2017

2 Forward Looking Statement 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," "anticipates," "plans," "expects," "indicates," "will," "intends," "potential," "suggests," "assuming," "designed" 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 ZX008 s potential as a treatment for seizures associated with Dravet syndrome and Lennox Gastaut Syndrome (LGS); the timing of results from ongoing and planned clinical trials; the timing and development plan for the Phase 3 clinical program for LGS; regulatory submission timelines for ZX008; the potential commercialization of ZX008; and Zogenix s financial position. The inclusion of forward-looking statements should not be regarded as a representation by Zogenix that any of its plans will be achieved. Actual results may differ from those set forth in this presentation due to the risks and uncertainties inherent in Zogenix's business, including, without limitation: the top-line data Zogenix reports from time to time is based on preliminary analysis of key efficacy and safety data, and such data may change following a more comprehensive review of the data related to the clinical trial and such top-line data may not accurately reflect the complete results of the trial, and the FDA may not agree with Zogenix s interpretation of such results; the uncertainties associated with the clinical development and regulatory approval of product candidates such as ZX008, including potential delays in the enrollment and completion of clinical trials and regulatory submissions; the potential that earlier clinical trials and studies 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, if approved, its commercial drug supplies; unexpected adverse side effects or inadequate therapeutic efficacy of ZX008 that could limit approval and/or commercialization, or that could result in recalls or product liability claims; Zogenix's ability to fully comply with numerous federal, state and local laws and regulatory requirements, as well as rules and regulations outside the United States, that apply to its product development activities; Fast Track designation may not result in an expedited regulatory review process; Zogenix s cash burn rate may be greater than anticipated; and other risks described in Zogenix's press releases as well as in public periodic filings with the Securities and Exchange Commission. 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 presentation to reflect events or circumstances after the date hereof. All forward-looking statements are qualified in their entirety by this cautionary statement.

3 Highly Focused on Developing and Commercializing Therapies for RARE CNS DISORDERS ZX008 (Low Dose Fenfluramine) for the Treatment of Uncontrolled Seizures DRAVET SYNDROME Phase 3 Program Underway Announced Positive Top Line Results in Study 1 LENNOX GASTAUT SYNDROME Targeting Phase 3 Trial Initiation Q4 2017

Dravet Syndrome: Catastrophic Illness Intractable, Severe Epilepsy Begins in infancy Pharmcoresistant Genetic epilepsy syndrome (SCN1A) Developmental encephalopathy Intellectual disability, ADHD, behavior, crouch gait Higher incidence of status epilepticus, SUDEP Rare, Orphan Disease Recent incidence study 1/15,700 births Can go undiagnosed or have late diagnosis No Effective Long-Term Treatments Exist Standard of care: Valproate, topiramate, levetiracetam, clobazam, clonazepam, stiripentol (EU) No approved drugs for Dravet syndrome in U.S. Sodium channel blockers (carbamazepine, phenytoin) make seizures worse 4

5 ZX008 Phase 3 Study 1 Design Study 1 is a prospective merged analysis of two identical double-blind, placebocontrolled studies ZX008-1501 (US/Canada) and ZX008-1502 (Europe/Australia) 6 WEEKS BASELINE OBSERVATION 2 WEEKS TITRATION 12 WEEKS MAINTENANCE ZX008 0.8 mg/kg/d n=40 Screening n = 119 Ages 2 18 1:1:1 Randomization ZX008 0.2 mg/kg/d n=39 Open Label Safety Study Placebo n=40 Maximum Daily Dose of 30mg

6 Study 1 Met Primary Efficacy Endpoint Study 1 met primary endpoint demonstrating ZX008, at a dose of 0.8 mg/kg/day, is superior to placebo as adjunctive therapy in the treatment of Dravet syndrome based on the change in the mean monthly convulsive seizure frequency (p<0.001) ZX008, at a dose of 0.2 mg/kg/day, also demonstrated superiority to placebo based on the same endpoint (p=0.019) % DIFFERENCE FROM PLACEBO IN REDUCTION IN MEAN MONTHLY CONVULSIVE SEIZURES (2 WK TITRATION + 12 WK MAINTENANCE PERIOD) PRIMARY ENDPOINT p<0.001 63.9% p=0.019 33.7% p-values are treatment compared with placebo group 0.8 mg/kg/day 0.2 mg/kg/day

7 Study 1 Convulsive Seizure Responder Rates 80% 70% 60% PROPORTION OF PATIENTS WHO ACHIEVED 50% AND 75% REDUCTION IN MEAN MONTHLY CONVULSIVE SEIZURES (2 WK TITRATION + 12 WK MAINTENANCE PERIOD) p<0.001 70.0% 50% 40% 30% 20% 10% 0% p=0.001 41.0% 7.5% 50% Reduction p=0.001 45.0% p=0.033 20.5% 2.5% 75% Reduction 0.8 mg/kg/day 0.2 mg/kg/day Placebo p-values calculated vs. placebo

Study 1 Longest Seizure Free Interval MEDIAN AND MEAN OF EACH PATIENT S LONGEST SEIZURE FREE INTERVAL (2 WK TITRATION + 12 WK MAINTENANCE PERIOD) 0.8 mg/kg/day 20.5 p<0.001 27.5 Median Mean 0.2 mg/kg/day 14.0 p=0.011 22.0 Median Mean Placebo 9.0 9.5 Median Mean 0 5 10 15 20 25 30 Days p-values are for median values vs. placebo 8

9 Study 1 Seizure Freedom/Near-Freedom Rates PROPORTION OF PATIENTS WHO EXPERIENCED ZERO (0) SEIZURES OR ONE (1) SEIZURE THROUGHOUT FULL TREATMENT PERIOD (2 WK TITRATION + 12 WK MAINTENANCE PERIOD) 0.8 mg/kg/day 7.5% 17.5% 0 Seizures 1 Seizure 0.2 mg/kg/day 7.7% 5.1% 0 Seizures 1 Seizure Placebo 0.0% 0.0% 0.0% 5.0% 10.0% 15.0% 20.0% 25.0% 30.0% Note: mean monthly seizure rate at baseline for all patients in Study 1 was 40/month

10 ZX008 Study 1 Safety Number of Subjects With at Least One Treatment Emergent Adverse Event (AEs) Number of Subjects With at Least One Treatment Emergent Serious Adverse Event (SAEs) Placebo (n=40) ZX008 0.2 mg (n=39) ZX008 0.8 mg (n=40) 26 (65.0%) 37 (94.9%) 38 (95.0%) 4 (10.0%) 4 (10.3%) 5 (12.5%) Prospective cardiac safety monitoring throughout the study demonstrated no clinical or echocardiographic evidence of cardiac valvulopathy or pulmonary hypertension. Generally well-tolerated with adverse events consistent with the known safety profile of fenfluramine. The incidence of treatment emergent adverse events was higher in treatment groups as compared to placebo; however, the incidence of treatment emergent serious adverse events was similar in all three groups. Five subjects in the 0.8 mg/kg/day group had an adverse event leading to study discontinuation, compared to zero in the other treatment groups.

Global Phase 3 Program in Dravet Syndrome ZX008 as adjunctive treatment for seizures in children and young adults with Dravet syndrome Study 1501 / Study 1502 Study 1504 Double-blind, randomized, placebocontrolled, 12-week treatment Two active doses (0.2 mg/kg/day, 0.8 mg/kg/day) & placebo U.S. Standard of Care; Stiripentol excluded Primary outcome: Change from baseline in frequency of monthly convulsive seizures FDA confirmation of adequate and well-controlled pivotal trial design Double-blind, randomized, placebocontrolled, 12-week treatment One active dose (0.5 mg/kg/day) & placebo EU Standard of Care; All patients on stiripentol Primary outcome: Change from baseline in frequency of monthly convulsive seizures FDA confirmation of adequate and well-controlled pivotal trial design All patients eligible to enter Study 1503: long-term, open-label, flexible-dose extension 11

12 ZX008 NDA Filing Strategy in Dravet Syndrome 2016 2017 2018 1501 1502 Study 1 top-line (n=119) Positive results announced Sep 29, 2017 PIVOTAL #1 (n=80) 1504 PIVOTAL #2 Study 1504 enrollment estimated to complete in Q4 2017 NDA SUBMISSION (Fast Track)

13 Commercial Manufacturing Readiness API sourcing & Bulk manufacturing Labeling & Packaging Specialty Pharmacy / Distribution Physician / Patient Room-temperature, oral solution (2.5 mg/ml) Proprietary, patent-pending synthesis Outsourced production via leading third party CMOs with GMP licensed facilities Commercial scale implemented for drug substance and product Registration batches completed CMC regulatory sections underway and scheduled to be completed in 2017

ZX008 Commercialization in Dravet Syndrome Full Global Commercialization Rights Retained High Touch, Targeted Commercial Effort Leadership Experienced in Rare Disease and Epilepsy Markets No approved products Majority of patients uncontrolled ~2,000 to 3,000 clinicians, majority are pediatric neurologists (1) Target sales force of 20-30 7.5 year orphan drug exclusivity; issued patents One approved product (stiripentol) Majority of patients uncontrolled Top 10 countries >90% of opportunity 15-30 key pediatric centers in major countries (1) 12 year orphan & pediatric investigational plan drug exclusivity (1) Company estimates 14

Lennox Gastaut Syndrome (LGS) Refractory, Debilitating Early-Onset Epilepsy Onset peaks 5-7 years of age Multiple seizure types, including drop seizures Cognitive impairment Characteristic EEG abnormality Underlying etiologies: 66% brain abnormalities, 33% unknown No known genetic abnormality identified Rare, Orphan Disease US Prevalence: ~30,000; 14,500-18,500 children EU Prevalence: >50,000; ~11,000 children No Effective Long-Term Treatment Exists Polypharmacy with AEDs is standard of care Six drugs approved in US but large unmet need persists 15

ZX008 in LGS: Interim Phase 2 Results Open Label, 20-Week, Dose Finding Trial of ZX008 as Add-on Anticonvulsive Therapy 13 patients to date (average age 11.4 years) with minimum of 12 weeks of treatment Failed a median of 5 antiepileptic therapies Receiving a median of 4 antiepileptic therapies At least 4 documented major motor seizures during 4-week baseline Dose-finding study design: All patients start at 0.2 mg/kg/d ZX008 Semi-forced step-titration design: patients who tolerate study drug but do not achieve 50% reduction in seizures step to next dose level Dose adjusted after 4 weeks at level: 0.2 mg/kg/day to 0.4 mg/kg/day to 0.8 mg/kg/day; max dose 30 mg/day Median Number of Seizures 70 60 50 40 30 20 10 0 Intent-to-Treat (ITT) Population Baseline Week 8 Week 12 Week 16 Week 20 7/13 (54%) Achieved at Least a 50% Reduction in Number of Major Motor Seizures Dose-Response is Emerging: 2-Fold Increase in Responders, 0.2 versus 0.4 mg/kg/d Most Common AEs: Decreased Appetite (3), Somnolence (3), Insomnia (2) Early Termination by 4 Patients 3 discontinued due to AEs 1 withdrew after loss of response following orthopedic surgery Lagae et al. American Epilepsy Society Annual Meeting, Houston, December 2016 16

17 ZX008 LGS Development Plan Single, global Phase 3 trial leveraging sites participating in the ZX008 Phase 3 program in Dravet syndrome IND accepted in April 2017 to enable Phase 3 initiation in Q4 2017 Trial design consistent with recent positive trial in Dravet syndrome Primary efficacy endpoint will be the mean change in the number of seizures that result in drops per 28 days during the treatment titration and maintenance periods compared with baseline Anticipated regulatory filing strategy is snda (U.S.) and MAA variation (EU) pending Dravet syndrome approval Orphan Drug Status received for both U.S. and EU during H1 2017

18 Focused on Developing and Commercializing Therapies for RARE CNS DISORDERS ZX008 Phase 3 Study 1 Top-Line Results Trial met primary endpoint of the change in the mean monthly convulsive seizure frequency All key secondary endpoints positive and demonstrated statistical significance