Background The Amref Alternative Rites of Passage (ARP) model was initiated in 2009. To date, about 20,000 girls have been supported by their communities to denounce female genital mutilation/cutting (FGM/C) and graduate into ‘maturity’ through ARP. While this intervention has been implemented for decades, there is limited evidence of its effectiveness in ending FGM/C. In order to ascertain the effectiveness of this intervention, Amref has developed a digital tracking tool to follow up on girls who have and haven’t gone through the ARP. The key research question is: what effect does ARP have on incidences of FGM/C, teenage pregnancy and child, early and forced marriages among adolescent girls and young women? Methods The study will adopt a stepped-wedge cluster randomised controlled trial design to assess the effectiveness of the ARP model on the incidence of FGM/C; teenage pregnancy; child, early and forced marriage; and educational attainment. We selected one cluster in Kajiado County where recent ARPs have been conducted as the intervention site at the beginning of the study and 3 wards/clusters in Narok County as control sites. Approximately 604 girls aged 10-18 years who reside in selected sites/clusters in Kajiado and Narok counties will be recruited and followed up for 3 years post-exposure. Quantitative data analysis will be conducted at bivariate and multivariate levels. Content/thematic analysis approach will be used to analyse qualitative data. Ethics and dissemination The study obtained ethical approval from the Amref Ethics and Scientific Review Committee (AMREF-ESRC P1051-2021). The findings of this study will be shared with local, national and regional stakeholders working in ending FGM/C, teenage pregnancy, and child, early and forced marriages. Registration – Pan-African Clinical Trials Registry (PACTR202208731662190).