Sexual assault is a global threat to adolescent health, but empowerment self-defense (ESD) interventions have shown promise for prevention. This study evaluated the joint implementation of a girls' ESD program and a concurrent boys' program, implemented via a cluster-randomized controlled trial in informal settlements of Nairobi, Kenya, from January 2016 to October 2018. Schools were randomized to the 12-h intervention or 2-h standard of care. Students were randomly sampled to complete surveys at baseline and again at 24 months post-intervention. A total of 3263 girls, ages 10-14, who completed both baseline and follow-up surveys were analyzed; weights were adjusted for dropout. At follow-up, 5.9% (n = 194/3263) of girls reported having been raped in the prior 12 months. Odds of reporting rape were not significantly different in the intervention versus SOC group (OR: 1.21; 95% CI (0.40, 5.21), p = 0.63). Secondary outcomes, social self-efficacy (OR: 1.08; 95% CI (0.95, 1.22), p = 0.22), emotional self-efficacy (OR 1.07; 95% CI (0.89, 1.29), p = 0.49), and academic self-efficacy (OR: 0.90; 95% CI (0.82, 1.00), p = 0.06) were not significantly different. Exploratory analyses of boys' victimization and perpetration are reported. This study improved on previous ESD studies in this setting with longitudinal follow-up of individuals and independent data collection. This study did not show an effect of the intervention on self-reported rape; findings should be interpreted cautiously due to limitations. Sexual assault rates are high in this young population, underscoring a dire need to implement and rigorously test sexual assault prevention interventions in this setting. The trial was registered with Clinical Trials.gov # NCT02771132. Version 3.1 registered on May 2017, first participant enrolled January 2017.