MediciNova, Inc. 2015 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

Tipelukast MN 001 MN 001 LOXL2 Cross linking of collagen and elastin fibrosis Collagen Type 1 CCR2 MCP 1 TIMP 1 MN 001 Reduces Gene Expression LOXL2 Collagen Type 1 CCR2 MCP 1 TIMP 1 MediciNova, Inc. 2015 More than 600 human subjects exposed to MN 001 Phase 2 study of MN 001 in asthma with positive results MN 001 was considered generally safe and well tolerated Pre clinical data shows anti fibrotic effect in a Dose Dependent Manner Improved NAFLD Activity Score (NAS) via a reduction in hepatocyte ballooning Reduced fibrosis area 15 MN 001 Data NAFLD Activity Score (NAS) % of fibrosis area Tipelukast MN 001 MediciNova, Inc. 2015 Timeline Progressive MS 16 Q2 2013: Submit New IND Amendment and New Protocol Q3 2013: FDA Approval of Protocol Study Initiation Q4 2013: Began Enrollment Q2 2015: Presentation at AAN Q2 2015: Completed Enrollment 2H 2016: Interim analysis 1H 2017: Final Results Progressive Multiple Sclerosis Progressive MS MediciNova, Inc. 2015 Timeline ALS 17 Amyotrophic Lateral Sclerosis (ALS) Lou Gehrig's Disease Q3 2014: Submit New ALS Protocol as IND Amendment Q3 2014: FDA Approval to Start Study Q4 2014: Began Enrollment Q2 2015: Presentation at AAN: Positive Interim Safety Review Q3 2015: Amended Protocol to include 60 Advanced ALS patients using non invasive ventilation (NIV) Q4 2015: Interim data MediciNova, Inc. 2015 Timeline NASH 18 Nonalcoholic Steatohepatitis (NASH) Tipelukast MN 001 Q1 2014: Positive preclinical data in NASH Q3 2014: Positive preclinical data in Advanced NASH Q4 2014: Present NASH data at AASLD and JDDW Q1 2015: Opened IND; FDA Approved Phase 2 Protocol Q1 2015: New Patent allowed for NASH Q2 2015: Fast Track designation granted ASAP: Initiate Phase 2 Study MediciNova, Inc. 2015 Timeline IPF 19 Q2 2014: Positive preclinical data in pulmonary fibrosis Q3 2014: Present data at ICLAF Q4 2014: Prepare Protocol Q4 2014: FDA granted Orphan drug designation to MN 001 for IPF Q1 2015: FDA Approved Phase 2 Protocol for moderate to severe IPF Q3 2015: Fast Track designation granted ASAP: Initiate Phase 2 Study Tipelukast MN 001 Idiopathic Pulmonary Fibrosis IPF MediciNova, Inc. 2015 20 MN 001 (tipelukast): 3 New Patents NASH: New Patent covers MN 001 (tipelukast) and MN 002 (a major metabolite of MN 001) for treatment of nonalcoholic steatohepatitis (NASH); Expires no earlier than Dec 2032 NAFLD: New P atent covers MN 001 (tipelukast) and MN 002 (a major metabolite of MN 001) for treatment of nonalcoholic fatty liver disease (NAFLD); Expires no earlier than Dec 2032 Liver Disorders: N ew P atent covers MN 001 (tipelukast) and MN 002 (a major metabolite of MN 001) for the treatment of steatosis , lobular inflammation, hepatic ballooning, hepatic scarring, and elevated liver hydroxyproline levels; Expires no earlier than Dec 2032 ASH (Alcoholic steatohepatitis) NASH (Nonalcoholic steatohepatitis) NAFLD (Nonalcoholic fatty liver disease) AFLD (Alcoholic fatty liver disease) Steatosis MediciNova, Inc. 2015 21 2014 ALS: New Protocol Submitted ALS: FDA Approval to Start Study ALS: Began Enrollment NASH: Positive Preclinical Data NASH: Presented at AASLD and JDDW IPF: Orphan Drug Designation Granted New Patents cover NAFLD, steatosis, and other liver disorders 2015 AAN Presentations for ALS and Progressive MS Progressive MS: Completed Enrollment ALS: Amended Protocol (Advanced ALS) ALS: Interim Data NASH: Opened IND; Protocol Approved, New Patent covers NASH, Fast Track IPF: FDA Approved Protocol, Fast Track NASH: Announce Next Steps IPF: Announce Next Steps 2016 Progressive MS: Interim Analysis 2017 Progressive MS: Final Results MN 166 Ibudilast Tipelukast MN 001 Timeline Summary MEDIC I NOVA

Fibrosis Fibrosis is the development of excess fibrous connective tissue in an organ Fibrosis is a result of inflammation, irritation, or healing (e.g. scar) Cross linking of collagen and elastin is the final step in fibrosis Cross linking of collagen and elastin fibrosis MediciNova, Inc. 2015 13 How does Fibrosis Develop? Genes Promoting Fibrosis LOXL2 Collagen Type 1 CCR2 MCP 1 TIMP 1 LOXL2 Cross linking of collagen and elastin fibrosis Collagen Type 1 CCR2 MCP 1 TIMP 1 MediciNova, Inc. 2015 14 How does MN 001 work?

MediciNova, Inc. 2015 MN 166 Phase 2 RRMS Data Significant attenuation of brain volume loss (p=0.035) Significant attenuation of conversion of acute lesions to persistent black holes (p=0.004) Sustained disability progression was significantly less likely (p=0.026) MN 166 Ongoing NIH funded Phase 2b study PPMS and SPMS study Trial to be completed in 1H 2017 9 MN 166: MS Data MediciNova, Inc. 2015 MN 166 Opioid Withdrawal Analgesia Phase 1b/2a Trial Reduced Subjective Opioid Withdrawal Scale (SOWS) Significantly reduced perspiring (p 0.05) and hot flashes (p 0.05), two components of SOWS MN 166 Opioid Self Administration Phase 2a Trial (INTERIM DATA) Significantly decreased the craving for heroin (p 0.05), cocaine (p 0.05), and tobacco (p 0.05) Significantly decreased the positive subjective effects of oxycodone measured by mean responses to statements such as I Feel High (p 0.05) and I Liked the Dose (p 0.05) MN 166 Methamphetamine Phase Ib Trial Significantly reduced perseverations (p=0.01) and variability in response times (p=0.006), suggesting a protective effect on sustained attention 10 MN 166: Addiction Data MediciNova, Inc. 2015 FDA Granted Orphan Drug Designation to MN 166 for Krabbe disease (June 2015) Krabbe disease is a rare genetic degenerative disorder for which there is no cure and is generally fatal before two years of age Only treatment option for Krabbe disease is hematopoietic stem cell transplantation, which has limited efficacy and potential risk to the patient MediciNova has O pen Investigational New Drug (IND) application with the Division of Neurology Products (DNP) for MN 166 FDA Approval would generate valuable Priority Review Voucher Rare Pediatric Disease Priority Review Voucher can be sold BioMarin sold its voucher to Regeneron for $67.5 million (July 2014) Retrophin sold its voucher to Sanofi for $245 million (May 2015) United Therapeutics sold its voucher to AbbVie for $350 million (August 2015) 11 MN 166: Krabbe Disease MediciNova, Inc. 2015 12 What is Fibrosis?

National Digestive Diseases Information Clearinghouse (NDDIC) 2. Allied Market Research 3. Coalition for Pulmonary Fibrosis 4. Research and Markets 5. Esbriet prescribing information 6. OFEV prescribing information IPF prevalence about 128,000 in the U.S. 3 (Orphan indication) Two thirds of IPF patients die within 5 years 3 IPF Market forecast: $1 Billion in 2017 4 Approved Drugs: Esbriet (pirfenidone) approved in October 2014; Esbriet Phase 3 studies enrolled mild to moderate IPF; No survival benefit shown 5 OFEV (nintedanib) approved in October 2014; Phase 3 studies enrolled mild to moderate IPF; No survival benefit shown 6 MediciNova, Inc. 2015 7 Tipelukast MN 001 Developing Novel Therapeutics MEDIC I NOVA MN 166 Ibudilast MediciNova, Inc. 2015 GLIAL CELL ATTENUATION Role of Glia: Type of macrophage Increases in number during brain damage Glial activation leads to neurodegeneration MIF Inhibition: Linked to attenuated disease progression in animal models of MS PDE inhibition Increases cAMP, reducing inflammation 8 How does MN 166 work?

We believe Progressive MS market is at least as large as RRMS market. Approved Drugs: NONE APPROVED for long term treatment of Progressive MS Amyotrophic Lateral Sclerosis (ALS) Lou Gehrig's Disease 1. Source: National Multiple Sclerosis Society 2. Source: ALS Association 3. Source: Cowen Co. estimate 4. Cochrane Database of Systematic Reviews Fatal: ALS Life expectancy is 2 5 years 2 ALS affects up to 30,000 people in the U.S. 2 (Orphan indication) Market opportunity: an effective new drug for ALS could generate sales $1 billion per year 3 Approved Drugs: RILUZOLE increases survival by only 2 3 months 4 MediciNova, Inc. 2015 6 Fibrotic Diseases Idiopathic Pulmonary Fibrosis IPF Nonalcoholic Steatohepatitis NASH NASH prevalence in the U.S. is 2 5% 1 Additional 10 20% have fatty liver due to being overweight or obese 1 NASH Market forecast: $1.6 billion by 2020 2 Approved Drugs: NO TREATMENT APPROVED 1.

Undue reliance should not be placed on these forward looking statements, which speak only as of September 25, 2015. MediciNova disclaims any intent or obligation to revise or update these forward looking statements. Forward Looking Statements MediciNova, Inc. 2015 Novel product candidates in clinical development with encouraging efficacy and safety data MN 166 (ibudilast) for the treatment of Neurology Diseases including Progressive MS, ALS, and Drug Dependence Approved in Japan in 1989 (post stroke dizziness and asthma) Large safety database MN 001 for the treatment of Fibrotic Diseases including NASH (nonalcoholic steatohepatitis) and IPF (idiopathic pulmonary fibrosis) MN 221 for the treatment of acute exacerbations of asthma Well capitalized Experienced management team 3 MediciNova Highlights MediciNova, Inc. 2015 4 MediciNova: Active Programs in Clinical Development MediciNova, Inc. 2015 5 Neurodegenerative Diseases Progressive Multiple Sclerosis Progressive MS MS affects more than 400,000 people in the U.S. and 2.3 million worldwide 1 Patients experience a diminished quality of life (e.g. fatigue, walking difficulties, weakness, pain, cognitive changes, depression) 1 Market opportunity: Total sales of RRMS drugs were $18 billion worldwide in 2014.

These forward looking statements involve a number of risks and uncertainties that may cause actual results or events to differ materially from those expressed or implied by such forward looking statements. Factors that may cause actual results or events to differ materially from those expressed or implied by these forward looking statements include, but are not limited to, risks of obtaining future partner or grant funding for development of MN 166, MN 221, MN 001, and MN 029 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, 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, 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 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 of expected filings with the regulatory authorities, 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, and the other risks and uncertainties described in MediciNova's filings with the Securities and Exchange Commission, including its annual report on Form 10 K for the year ended December 31, 2014 and its subsequent periodic reports on Forms 10 Q and 8 K.

These forward looking statements include, without limitation, statements regarding the future development and efficacy of MN 166, MN 221, MN 001, and MN 029. 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, considering, planning or similar expressions.

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.

MediciNova, Inc. 2015 Developing Novel Therapeutics for the Treatment of Serious Diseases with Unmet Medical Needs Exhibit 99.1 MediciNova, Inc. 2015 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.