BACKGROUND: Violence against children in schools is a global public health problem. There is growing evidence that school-based interventions can be effective in reducing violence against children in schools. However, there is little evidence on the long-term impact of such interventions. The Good School Toolkit, developed by Raising Voices, a Uganda-based nonprofit organization, is a whole-school violence prevention intervention that aims to change the operational culture of primary schools. In 2014, the Good School Toolkit was evaluated through a cluster randomized controlled trial (Good Schools Study) and found to reduce teacher-to-student and student-to-student violence. OBJECTIVE: This protocol describes quantitative analyses to explore long-term outcomes of the Good School Toolkit intervention among adolescents in Uganda, including the extent to which it is associated with peer-violence victimization (primary outcome) and peer-violence perpetration, intimate-partner violence, acceptance of teacher-violence, equitable gender attitudes, agency, self-regulation, peer connectedness, social assets, psychological assets, and retention in school (secondary outcomes). METHODS: This is a nonrandomized quasi-experimental 4-year follow-up study of adolescents who attended the 42 Good Schools Study primary schools in 2014; 21 schools initiated the Good School Toolkit intervention during the trial from 2012, and 19 schools initiated the intervention after the trial (during the later delivery phase) from 2015; 2 schools did not implement the intervention. Students in the final school grade (Primary 7) during 2014 of the 19 primary schools in the later delivery phase are expected to have left school prior to toolkit delivery in 2015. Wave 1 data were collected in 2014 from 3431 grade Primary 5 to Primary 7 school students aged 11-14 years; these students were followed up in 2018-2019 when aged 16-19 years and invited to participate in the Wave 2 survey. Data were collected in face-to-face interviews by trained Ugandan field researchers. Toolkit exposure groups are defined as exposed during the Good Schools Study trial (from 2012), as exposed during later delivery (from 2015), or not exposed including those expected to have completed Primary 7 prior to later delivery or from the 2 schools that did not implement the toolkit. Associations between outcomes at Wave 2 and toolkit exposure groups will be analyzed using mixed-effect multivariable logistic and linear regression models for binary and continuous outcomes, respectively. This analysis is exploratory and aims to generate hypotheses on if, and under what circumstances, the toolkit influences later adolescent outcomes. RESULTS: Data collection was completed in August 2019. CONCLUSIONS: To our knowledge, this is the first long-term follow-up study of adolescents exposed to a school-based violence-prevention intervention in sub-Saharan Africa. If the intervention reduces violence and improves other outcomes in later adolescence, then this study supports primary school interventions as key to achieving long-term population impacts. The pattern of effects will inform where reinforced or additional interventions are needed. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/20940.