Although inclusive education policies conflict with punitive discipline measures, inclusion in mainstream schools may coexist with or allow such exclusionary punitive discipline. In Latin America, however, there is scarce research on how punitive measures are distributed, and if and how they affect students with disabilities enrolled in regular school settings. The purpose of this study was to characterize the occurrence of punitive exclusionary practices among students with disabilities enrolled in mainstream schools. We analysed reports from a national sample of Chilean students (N = 447,697) and parents on the frequency of punitive exclusionary discipline practices to identify the contribution of individual, classroom and school factors to student exclusion from general education settings. Individual characteristics included different disability groups. Multilevel logistic regression results consistently showed that students with ADHD were more likely to receive disciplinary exclusions, both in primary and in high school, with an odds-ratio increase from 30% to nearly 150%, with higher rates for low-SES students with ADHD. These findings suggest that in Chile, student-level factors of gender, class and disability are strongly associated with exclusionary punitive discipline in schools. We discuss the intersectional dynamics of gender, class, race and disability in disciplinary processes of exclusion.