BACKGROUND: Zambian adolescent girls and young women (AGYW, age 15–24) experience a disproportionate burden of HIV and unintended pregnancy. Sports-based interventions, which affect sexual health behaviors via improving sexual and reproductive empowerment, may be an innovative and effective approach for promoting HIV and unintended pregnancy prevention. We sought to evaluate the impact of a peer-led, sports-based intervention on sexual and reproductive empowerment among in-school Zambian adolescent girls and young women. METHODS: Data come from the ‘SKILLZ’ study, a cluster randomized controlled trial evaluating the impact of a peer-led, sports-based health education program. Sexual and reproductive empowerment, a secondary outcome of SKILLZ, was measured via the 23-item Sexual and Reproductive Empowerment for adolescents and young adults scale (range 0–92, higher = more sexual and reproductive empowerment) three times over approximately 24 months. We conducted a difference-in-differences analysis to evaluate intervention impact over time. RESULTS: The study enrolled 2,153 AGYW (1134 intervention; 1019 control) across 46 secondary schools in Lusaka. Median age at baseline was 17; participants were largely unmarried (96%), with 20% reporting any sexual activity. By endline, nearly 40% reported being sexually active. Between baseline and midline, attending an intervention school was associated with a 6.21-point increase in overall score calculated using the imputed sample (standard error [SE]: 0.75, p < 0.001) compared to being in a control school (6.75% change). At endline, being in an intervention school was associated with a 5.12-point increase in the Sexual and Reproductive Empowerment overall score (SE: 0.71, p < 0.001; 5.57% change)). Among sexually active AGYW, being in an intervention school was associated with a 7.78-point (SE: 1.17, p < 0.001) and 4.64-point increase (SE: 0.93, p < 0.001) from the baseline to the midline and endline rounds, respectively (8.46% and 5.04% change, respectively). CONCLUSION: The intervention moderately impacted Sexual and Reproductive Empowerment scores; results were magnified among sexually active AGYW. Given adolescence is a critical period for sexuality and gender programming, as well as for sexual debut, empowerment interventions at schools may support downstream sexual health behaviors that will impact the life-course of AGYW. TRIAL REGISTRATION: This study was registered in ClinicalTrials.gov (NCT04429061) on March 17th, 2020. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12978-025-02046-6.