The delivery of comprehensive sexuality education to adolescents at school is recognized as a long-term strategy to support adolescent health. Suboptimal sexual and reproductive health (SRH) outcomes among South African adolescents necessitate the ongoing development and optimization of SRH education and promotion models. We conducted a cluster-randomized controlled trial amongst secondary schools (n = 38) in Cape Town, South Africa, to evaluate a sport-based, near-peer-led SRH curriculum, SKILLZ, amongst female learners (n = 2791). Biomedical (sexually transmitted infections [STIs], human immunodeficiency virus [HIV] and pregnancy) and socio-behavioural (social support, gender norms and self-concept) outcomes were assessed pre and post intervention. Attendance at SKILLZ was low and intervention participants did not show an improvement in SRH outcomes, with HIV and pregnancy incidence remaining stable and STI prevalence remaining high and increasing in both control and intervention arms. Although evidence of positive socio-behavioural measures was present at baseline, participants with high attendance showed further improvement in positive gender norms. SKILLZ did not demonstrate the capacity to significantly impact clinical SRH outcomes. Modest improvements in outcomes amongst high attenders suggest that the impact may be possible with improved attendance; however, in the absence of optimal attendance, alternative intervention strategies may be required to improve SRH outcomes amongst adolescents.