MediciNova, Inc. 2013 Statements in this presentation that are not historical in nature constitute forward looking statements within the meaning of the safe harbor provisions of the Private Securities Litigation Reform A

(2) A non addictive treatment would fill an unmet need in this large market MN 166 (ibudilast): MN 166 (ibudilast): A Novel Oral Therapy A Novel Oral Therapy for the Treatment of for the Treatment of Progressive Multiple Sclerosis (MS) Progressive Multiple Sclerosis (MS) 24 25 MN 166 (ibudilast): The Promise in Progressive MS MN 166 (ibudilast) is a small molecule with established safety 297 patient, two year Phase 2 clinical trial completed in MS Significant dose related improvements in disability progression and MRI outcomes (whole brain atrophy, black hole formation) Results indicated that MN 166 (ibudilast) is best suited to treat Progressive MS Glial neuronal activation cycle leads to underlying progressive neurodegeneration MIF knock out reduces the neuropathological and clinical disability sequelae in animal models Phase 2b development of MN 166 (ibudilast) for the treatment of Progressive MS via Academic Investigator/Government agency/MS society/MediciNova consortium(s) and grant funding MediciNova, Inc. 2013 26 MN 166 (ibudilast) Phase 2 Multiple Sclerosis Trial MediciNova, Inc. 2013 27 Placebo 30 mg/day Low Dose Group 60 mg/day High Dose Group Patient Subset % Brain Volume Change % Brain Volume Change Magnitude of Effect % Brain Volume Change Magnitude of Effect RRMS 1.2 1.1 8% less 0.8 33% less** SPMS 1.0 0.7 30% less 0.44 56% less MN 166 (ibudilast) Phase 2 Multiple Sclerosis (MS) Trial Mean change ** p=0.035 Whole Brain Atrophy Endpoint in Secondary Progressive MS (SPMS) Patients RRMS = Relapsing Remitting MS SPMS = Secondary Progressive MS MediciNova, Inc. 2013 28 Placebo 30 mg/day Low Dose Group 60 mg/day High Dose Group Patient Subset % Brain Volume Change % Brain Volume Change Magnitude of Effect % Brain Volume Change Magnitude of Effect RRMS 1.2 1.1 8% less 0.8 33% less** SPMS 1.0 0.7 30% less 0.44 56% less MediciNova is pursuing grant funding to support Phase 2b clinical trial(s) treating Progressive MS with MN 166 (ibudilast) MN 166 (ibudilast) Phase 2 Multiple Sclerosis (MS) Trial Mean change ** p=0.035 Whole Brain Atrophy Endpoint in Secondary Progressive MS (SPMS) Patients RRMS = Relapsing Remitting MS SPMS = Secondary Progressive MS MediciNova, Inc. 2013 MN 166 (ibudilast) Clinical Trials MN 166 (ibudilast) is advancing in multiple Phase 2 programs 29 GRANT FUNDED CLINICAL DEVELOPMENT MODEL MediciNova, Inc. 2013 30 Key Milestones for 2013 2014 MAJOR NEAR TERM VALUE INFLECTION POINTS 2H:2013 2H:2013 2H:2013 2H:2014 Clinical Milestones Timing Results of Phase 1b UCLA methamphetamine trial 1H:2013 Commence Phase 2 UCLA methamphetamine trial Announce grant funding for Phase 2b trial treating progressive MS with ibudilast Results of Phase 2a MOH pain trial Results of Phase 2a opioid dependence trial Results of Phase 2 methamphetamine trial 2H:2014 MediciNova, Inc. 2013 31 MN 166 (ibudilast) Program Patents * U.S. patent expiration does not include Waxman Hatch patent term restoration (industry average = 4.5 years) Patent Exclusivity Patent Exclusivity Method of Use Composition of Matter Addiction US Exp. 2030 EU Exp. 2026 AV1013 US Exp. 2027 EU Pending Progressive Multiple Sclerosis US Exp. 2029 EU Exp. 2028 AV1013 Enantiomer US Exp. 2030 EU Pending Neuropathic Pain US Exp. 2025 EU Pending 2 nd Generation Analogs Pending Acute Sub Chronic Pain US Pending EU Exp. 2028 Anxiety Traumatic Brain Injury / PTSD Pending Ibudilast + Immunomodulator for MS Pending MOH Pain Pending MediciNova, Inc. 2013 32 Leadership Years Experience Background Yuichi Iwaki, MD, PhD Yuichi Iwaki, MD, PhD President CEO, Founder 36 Professor at USC, formerly Professor at University of Pittsburgh; Advisor to JAFCO, Tanabe Michael Coffee Michael Coffee Chief Business Officer 28 Avigen, Amarin Corp., Elan Pharmaceuticals, N.A., Athena Neurosciences Kirk Johnson, PhD Kirk Johnson, PhD Chief Scientific Officer 23 Avigen, Genesoft Pharmaceuticals, Chiron Corporation (Novartis San Francisco) Kazuko Matsuda, MD, PhD, MPH Kazuko Matsuda, MD, PhD, MPH Chief Medical Officer 22 Assistant Professor USC, Keck School of Medicine; Children s Hospital Los Angeles Masatsune Okajima, CMA Masatsune Okajima, CMA VP, Head of Japanese Office 21 Daiwa Securities SMBC, Sumitomo Capital Securities, Sumitomo Bank Michael Gennaro, CPA, MBA Michael Gennaro, CPA, MBA Chief Financial Officer 38 Partner at FLG Partners, Sylantro Systems, Inverse Network Technology, Novell, Piiceon, Verticom Management Team with Global Experience

September 2012 ~353,000 individuals used methamphetamine in the past month ~70,600 patients seek treatment (20%) 6 month, initial course of treatment is recommended at ~$1,000/month 353,000 x 0.20 x $1000/month x 6 months $400 million market MediciNova, Inc. 2013 23 US Opioid Addiction Market US Market Opportunity for Opioid Addiction (1) Reckitt Benckiser Annual Report, 2012; Assumes 1 = 1.55 USD (2) Substance Abuse and Mental Health Services Administration's (SAMHSA) 2011 National Survey on Drug Use and Health Current market for opioid addiction is well established with substitution therapeutic agents such as Subutex/Suboxone with worldwide sales of ~$1.3B (1) in 2012 Approximately 1.4 million people with nonmedical pain reliever addiction and approximately 369,000 heroin addicts in the U.S.

MAJOR UNMET NEED FOR NOVEL TARGETS AND DIFFERENTIATED THERAPEUTICS MediciNova, Inc. 2013 22 US Methamphetamine Addiction Market US Market Opportunity of Methamphetamine Addiction (1) (1) Dr. Phil Skolnick, Director, Division of Pharmacotherapies Medical Consequences of Drug Abuse, NIDA; 2010 NSDUH survey; Neuropsychiatric R D Conference, San Francisco, CA.

Note: One outlier subject in the 80 mg/day group was excluded from the Total SOWS score analysis. MediciNova, Inc. 2013 20 MN 166 (ibudilast) Phase 2a Trial: Effects of MN 166 (ibudilast) on Oxycodone Self Administration in Opioid Abusers Trial Design n = 24 Prescription opioid drug abusers (including OxyContin, Vicodin, Percocet) or heroin Randomized, placebo controlled, double blind Inpatient study; two 20 day cross over periods in clinic where patients detox test self administration when on Placebo or 100 mg/day of MN 166 (ibudilast) Objective: Assess effect of MN 166 (ibudilast) on craving and self administration effects Partners Timing Trial commenced at end of 2012 Trial completion expected 2H:2014 MediciNova, Inc. 2013 21 Addiction Competitive Landscape No pharmaceutical treatment approved for methamphetamine addiction Available therapeutics for treating opioid addiction have limited efficacy and face increasing clinical regulatory scrutiny Buprenorphine buprenorphine/naloxone combination (Subutex Suboxone): Potential for abuse, tolerance and addiction Therapeutic effects reach a plateau at higher doses Suboxone pills recently removed from shelves, highlighting the need for safer alternatives Naltrexone: Precipitates withdrawal symptoms resulting in poor patient compliance Source: Wall Street Equity Research, NIDA, Curr Drug Abuse Rev.

FDA for the treatment of methamphetamine addiction U.S. Patent protection until at least 2030 for addiction and 2029 for progressive multiple sclerosis (MS) MN 166 (ibudilast) Overview MediciNova, Inc. 2013 MN 166 (ibudilast) Target Action Molecular MIF (macrophage migration inhibitory factor) PDE 10, PDE 4 12 ibudilast ibudilast pro inflammation via CD74/CXCR2,4 receptors degradation of cAMP ( cGMP) MediciNova, Inc. 2013 MN 166 (ibudilast) Target Action Cellular 13 Withdrawal symptoms, drug seeking and relapse associated with drug addiction; Neuropathology in drug addiction progressive MS ibudilast ibudilast An umbrella of cellular action covering the disease indications PDE 4 , 10 MIF Silence Activated Glia interrupt glial neuronal viscous cycle Glial cell activation is associated with key features of drug addiction MediciNova, Inc. 2013 14 MN 166 (ibudilast) Methamphetamine (MA) Phase 1b Trial Trial Design n = 11 Non treatment seeking MA dependent subjects Double blind, placebo controlled ~1 month inpatient hospitalization Dosing: One week each of Placebo, 40 mg/day, 100 mg/day Safety/Efficacy Measurements: Cardiovascular response to 15, 30 mg IV MA Cognitive Subjective effects Partners Status: Completed Data presented in June 2013 at CPDD* College of Problems of Drug Dependence MediciNova, Inc. 2013 15 MN 166 (ibudilast) Methamphetamine Phase 1b Trial Data presented at Annual CPDD Meeting in June 2013 Safety: Phase 1b trial established safety of co administration of methamphetamine and MN 166 (ibudilast) in doses up to 100 mg/day Enables 100 mg/day dosing for Phase 2 outpatient trials 15 16 MN 166 (ibudilast) Methamphetamine Phase 1b Trial 16 p=0.01 Efficacy: Conner s Continuous Performance Test II (CPT II) is a measure of sustained attention MN 166 (ibudilast) significantly reduced perseverations and variability in response times MN 166 (ibudilast) may have a protective effect on sustained attention Note: Perseveration is a reaction time that is less than 100 ms; Variability is a measure of response speed consistency MediciNova, Inc. 2013 17 MN 166 (ibudilast) Phase 2 Trial for Methamphetamine Addiction Trial Design n = 140 (seek to increase to 160) Treatment seeking volunteers Randomized, double blind, placebo controlled 1:1 Randomization with placebo or 100 mg/day of MN 166 (ibudilast) 12 week outpatient study Primary endpoint is methamphetamine abstinence during final two weeks of treatment; NIDA and FDA preferred endpoint Partners Timing Trial to commence 2H:2013 MediciNova, Inc. 2013 18 MN 166 (ibudilast) Phase 1b/2a Trial: Opioid Withdrawal Analgesia Trial Design n = 30 Heroin dependent subjects; 3 week inpatient setting Double blind, placebo controlled Week One: All subjects on morphine (30 mg/day) and Placebo Week Two: All subjects on morphine (30 mg/day) and either Placebo, 40 mg/day, or 80 mg/day of MN 166 (ibudilast) Week Three: Subjects continue on either Placebo, 40 mg/day, or 80 mg/day of MN 166 (ibudilast) with morphine removed Objective: Safety/tolerability/PK and preliminary efficacy for opiate withdrawal and analgesia Partners Status: Completed Completed end 2010 Results were presented at AAN in March 2013 *American Academy of Neurology MediciNova, Inc. 2013 MN 166 (ibudilast) Phase 1b/2a Trial: Ibudilast Effect on Primary Outcome Subjective Opioid Withdrawal Scale (SOWS) 19 Individual Measurements of SOWS Composite Primary Endpoint = Total SOWS score as a function of ibudilast dose Opioid related pupil constriction was greater in the 80 mg/day ibudilast group compared to the placebo group (p 0.05) suggesting lessened tolerance development.

Times are time difference between steroid dose and study drug. Data is from Phase 2b trial of MN 221 in acute exacerbations of asthma. Based on Phase 2b data, the ideal time to administer MN 221 is after the patient has not responded to standard of care for more than 3 4 hours. MN 166 (ibudilast): MN 166 (ibudilast): A Novel Oral Therapy for the A Novel Oral Therapy for the Treatment of Methamphetamine and Treatment of Methamphetamine and Opioid Addiction Opioid Addiction 10 MediciNova, Inc. 2013 11 Non addictive, orally administered small molecule NCE in U.S. and Europe: NCE exclusivity / Data exclusivity Large safety database with over 3.2M patient exposures in Japan Primary use is in cerebrovascular disorders (post stroke dizziness) Pharmacokinetics (PK) enable once or twice daily dosing Unique mechanism of action Encouraging Phase 1/2 data in targeted CNS indications with major unmet medical needs Received Fast Track designation from U.S.

Source: National Center for Health Statistics / CDC, National Hospital Discharge Survey MediciNova, Inc. 2013 1. API Manufacturing requirements of FDA Kissei, our API supplier, is addressing requirements Approximately 6 month duration 2. Clinical development work including: Dose regimen optimization Revision and validation of acute asthma exacerbation trial Primary endpoint will include hospitalization, consistent with FDA guidance 8 Next Steps for MN 221: Based on End of Phase 2 meeting with FDA MediciNova, Inc. 2013 9 MN 221: Impact of Dose Timing Note: Treatment Failure is hospitalization or return ER visit due to asthma.

Completed four Phase 2 clinical trials in asthma or AEA and two Phase 1b/2a clinical trials in COPD New method of use patent may significantly extend market exclusivity with patent protection until at least 2030 in U.S. Had an End of Phase 2 meeting with FDA MN 221 (bedoradrine) Overview MediciNova, Inc. 2013 7 MN 221 (bedoradrine) Overview Acute Asthma Treatment Flow in Emergency Departments in the U.S.

Had an End of Phase 2 meeting with FDA Newly issued patent Well capitalized Experienced management team 3 MediciNova Highlights MediciNova, Inc. 2013 MediciNova: Active Programs in Clinical Development 4 MN 221 (bedoradrine): MN 221 (bedoradrine): A Novel Intravenous Treatment for A Novel Intravenous Treatment for Acute Exacerbations of Asthma Acute Exacerbations of Asthma 5 MediciNova, Inc. 2013 6 NCE (new chemical entity), small molecule, beta 2 adrenergic receptor agonist in iv form In development for the treatment of Acute Exacerbations of Asthma (AEA) adjunctive to standard of care Licensed from Kissei Pharmaceutical Co., Ltd.

You are cautioned not to place undue reliance on these forward looking statements, which speak only as of July 17, 2013. MediciNova disclaims any intent or obligation to revise or update these forward looking statements. Forward Looking Statements MediciNova, Inc. 2013 Two novel product candidates in clinical development, both with encouraging efficacy and safety data MN 166 (ibudilast) for the treatment of drug addiction progressive MS Licensed from Kyorin Pharmaceuticals Two Phase 2 studies (methamphetamine and opioid addiction) Two progressive MS trials (pending grant funding) Newly issued patents (addiction and Progressive MS) MN 221 for the treatment of acute exacerbations of asthma Licensed from Kissei Pharmaceutical Co., Ltd.

These forward looking statements may be preceded by, followed by or otherwise include the words believes, expects, anticipates, intends, estimates, projects, can, could, may, will, would, or similar expressions. Actual results or events may differ materially from those expressed or implied in any forward looking statements due to various factors, including the risks of obtaining future partner or grant funding for development of MN 166 and MN 221 and risks of raising sufficient capital when needed to fund MediciNova s operations and contribution to clinical development, risks and uncertainties inherent in clinical trials, including the potential cost, expected timing and risks associated with clinical trials designed to meet FDA guidance and the viability of further development considering these factors, product development and commercialization risks, risks associated with the reliance on third parties to sponsor and fund clinical trials, risks regarding intellectual property rights in product candidates and the ability to defend and enforce such intellectual property rights, the uncertainty of whether the results of clinical trials will be predictive of results in later stages of product development, the risk of delays or failure to obtain or maintain regulatory approval, the risk of failure of the third parties upon whom MediciNova relies to conduct its clinical trials and manufacture its product candidates to perform as expected, the risk of increased cost and delays due to delays in the commencement, enrollment, completion or analysis of clinical trials or significant issues regarding the adequacy of clinical trial designs or the execution of clinical trials and the timing, cost and design of future clinical trials and research activities; the timing of expected filings with regulatory authorities; MediciNova s failure to execute strategic plans or strategies successfully; MediciNova s collaborations with third parties; the availability of funds to complete product development plans and MediciNova s ability to obtain third party funding for programs and raise sufficient capital when needed; intellectual property or contract rights; and the other risks and uncertainties described in MediciNova s filings with the Securities and Exchange Commission, including MediciNova s annual report on Form 10 K for the year ended December 31, 2012 and its subsequent periodic reports on Forms 10 Q and 8 K.

Developing Novel Therapeutics for the Treatment of Serious Diseases with Unmet Medical Needs Exhibit 99.1 MediciNova, Inc. 2013 Statements in this presentation that are not historical in nature constitute forward looking statements within the meaning of the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. These forward looking statements include statements regarding MediciNova s clinical trials supporting the safety and efficacy of its product candidates and the potential novelty of such product candidates as treatments for disease, plans and objectives for clinical trials and product development, strategies, future performance, expectations, assumptions, financial condition, liquidity and capital resources.