Introduction: Psychoactive substance use among adolescents influences behavioral and cognitive processes and is associated with adolescents' performance in school. We therefore sought to investigate association of PASU with adolescents' school performance. Methods: We employed quantitative methods of data collection and analysis. To test the substance use-school performance association, we specified and estimated fixed effects hierarchical linear models (HLMs). We nested the data in their respective four regions of Uganda. Results: Model estimates show that only alcohol use had significant t-values in association with school performance (b = 1.15, SE = 0.32, t = 3.83, p = 0.029 for beer use; b = 0.82, SE = 0.18, t = 4.49, p < 0.001 for wines; and b = 0.89, SE = 0.19, t = 4.53, p< 0.001 for spirits). Conclusions: Alcohol use significantly contributed to the model estimating association between PASU and adolescents' school performance.