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Abstract Background Despite a variety of mainly school-driven prevention strategies, the number of adolescent pregnancies in Rwanda is worryingly high and is even expected to increase. The aim of this study is to empower Kirehe secondary school students aged 15–19 years old in sexual and reproductive health (SRH) by developing a peer education program. Methods A combination of quantitative and qualitative research will be used. A pre- and post-survey will examine adolescents’ knowledge and attitudes regarding SRH. In addition, six focus group interviews will explore these knowledge, attitudes but also SRH needs more in depth. Based on the obtained information, and after retrieving experts’ input, a peer education program is being developed in which Midwifery students obtain training in SRH and educational skills (= first train-the-trainer module). In turn, these students will educate and train a selected group of secondary school students (= second train the trainer module). Finally, these trained in-school students can act as reliable peers for other in-school students in the context of SRH. Discussion The project will contribute to 1) more independent and thoughtful decisions in contraception and sexual behavior, and consequently less adolescent pregnancies, and 2) the reinforcement of the Rwandan Midwifery education. Trial registration University of Rwanda, College of Medicine and Health Sciences, Institutional Review Board, Approval No 158/CMHS IRB/2019.