Racial discrimination has been associated with worse health status and risky health behavior. Understanding the relationship between racial-based bullying (RBB) - an overlap of bullying and interpersonal racial discrimination - and substance use can guide school-based actions to prevent bullying and substance use, but investigations rarely involve Brazilian students. We used data from the National Survey of School Health (PeNSE) 2015, which included 102,072 ninth-grade students from the capital and inland cities in the five regions of Brazil. Students self-reported their race/skin color according to the Brazilian official census. We explored racial and recent RBB differences in recent use of alcohol, tobacco, and other substances [marijuana, cocaine, crack, sniffed glue, loló/lança-perfume (ether and chloroform blend)] by comparing prevalence ratios (estimated with quasi-Poisson, crude, and adjusted models by demographic and socioeconomic characteristics) obtained from analyses of imputed data and complete case. We found that RBB prevalence increased according to racial categories associated with darker skin tones; racial differences in the prevalence of RBB were greater among girls than boys. Girls from all racial groups consistently had a higher prevalence of alcohol use than boys. RBB partially explained the recent use of alcohol and tobacco for the minority racial groups and was not associated with the use of other substances. School-based actions should explicitly incorporate anti-racist goals as strategies for substance use prevention, giving particular attention to gender issues in racial discrimination and alcohol use.