Abstract Background Alcohol and illicit drug use has been recognized as a growing problem among adolescents in Botswana. Little is known about factors affecting alcohol and drug use among Botswana’s secondary school students. To aid the design and implementation of effective public health interventions, we sought to determine the prevalence of alcohol and drug use in secondary school students in urban and peri-urban areas of Botswana, and to evaluate risk and protective factors for substance use. Methods We performed a 72-item cross-sectional survey of students in 17 public secondary schools in Gaborone, Lobatse, Molepolole and Mochudi, Botswana. The World Health Organization’s (WHO) Alcohol Use Disorder Identification Test (AUDIT) was used to define hazardous drinking behavior. Using Jessor’s Problem Behavior Theory (PBT) as our conceptual framework, we culturally-adapted items from previously validated tools to measure risk and protective factors for alcohol and drug use. Between-group differences of risk and protective factors were compared using univariate binomial and multinomial-ordinal logit analysis. Relative risks of alcohol and drug use by demographic, high risks and low protections were calculated. Multivariate ordinal-multinomial cumulative logit analysis, multivariate nominal-multinomial logit analysis, and binominal logit analysis were used to build models illustrating the relationship between risk and protective factors and student alcohol and illicit drug use. Clustered data was adjusted for in all analyses using Generalized Estimating Equations (GEE) methods. Results Of the 1936 students surveyed, 816 (42.1%) reported alcohol use, and 434 (22.4%) met criteria for hazardous alcohol use. Illicit drug use was reported by 324 students (16.7%), with motokwane (marijuana) being the most commonly used drug. Risk factors more strongly associated with alcohol and drug use were reported alcohol availability, individual and social vulnerability factors, and poor peer modeling. Individual and social controls protections appear to mitigate risk of student alcohol and drug use. Conclusions Alcohol and illicit drug use is prevalent among secondary school students in Botswana. Our data suggest that interventions that reduce the availability of alcohol and drugs and that build greater support networks for adolescents may be most helpful in decreasing alcohol and drug use among secondary school students in Botswana.