Background: The burden of substance use in Kenya is significant. The objective of this study was to systematically summarize existing literature on substance use in Kenya, identify research gaps, and provide directions for future research. Methods: This systematic review was conducted in line with the PRISMA guidelines. We conducted a search of 5 bibliographic databases (PubMed, PsychINFO, Web of Science, Cumulative Index of Nursing and Allied Professionals (CINAHL) and Cochrane Library) until 20 August 2020. In addition we searched all the volumes of the official journal of the National Authority for the Campaign Against Alcohol & Drug Abuse (the African Journal of Alcohol and Drug Abuse). The results of eligible studies have been summarized descriptively and organized by the three broad categories: (1) Studies evaluating the epidemiology of substance use, (2) studies evaluating interventions and programs, and (3) qualitative studies exploring various themes on substance use. The quality of the included studies was assessed with the Quality Assessment Tool for Studies with Diverse Designs.Results: Of the 185 studies that were eligible for inclusion, 144 investigated the epidemiology of substance use, 23 qualitatively explored various substance use related themes, and 18 evaluated substance use interventions and programs. Key evidence gaps emerged. Firstly, vulnerable populations such as police officers, pregnant women, health care workers and persons with physical disability had been under-represented within the epidemiological and qualitative work. Secondly, no intervention study had been conducted among children and adolescents. Thirdly, most interventions had focused on alcohol to the exclusion of other prevalent substances such as tobacco and cannabis. Finally, little had been done to evaluate digital and population-level interventions. Conclusions: The results of this systematic review provide important directions for future substance use research in Kenya. Systematic review registration: PROSPERO: CRD42020203717