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Purpose We tested whether the Good School Toolkit reduces physical violence from peers and school staff toward students with and without disabilities in Ugandan primary schools. Methods We conducted a cluster randomized controlled trial, with data collected via cross-sectional surveys in 2012 and 2014. Forty-two primary schools in Luwero District, Uganda, were randomly assigned to receive the Good School Toolkit for 18 months, or to a waitlisted control group. The primary outcome was past week physical violence from school staff, measured by primary 5, 6, and 7 students' (aged 11–14 years) self-reports using the International Society for the Prevention of Child Abuse and Neglect Child Abuse Screening Tool-Child Institutional. Disability was assessed through the six Short Set Washington Group questions on functioning. Analyses were by intention to treat. Results At endline, 53% of control group students with no functional difficulties reported violence from peers or school staff, versus 84% of students with a disability. Prevalence of past week physical violence from school staff was lower in intervention schools than in the control schools after the intervention, in students with no functional difficulties (adjusted odds ratio [aOR] = .41, 95% confidence interval [CI .26–.65]), students with some functional difficulties (aOR = .36, 95% CI .21–.63), and students with disabilities (aOR = .29, 95% CI .14–.59). The intervention also reduced violence from peers in young adolescents, with no evidence of a difference in effect by disability status. Conclusions The Good School Toolkit is an effective intervention to reduce violence perpetrated by peers and school staff against young adolescents with disabilities in Ugandan primary schools.