Adolescents in Kenya face a high burden of sexual and reproductive health (SRH) challenges, including early pregnancy, sexually transmitted infections and limited access to accurate sexuality education. While school-based comprehensive sexuality education (SBCSE) has shown promise globally, its implementation in Kenya has faced significant barriers, including cultural resistance and lack of trained personnel. To address these gaps, the Afya Kesho (‘Health for Tomorrow’) programme introduces an innovative, animation-based, school-integrated and community-integrated comprehensive sexuality education curriculum aimed at enhancing adolescent SRH knowledge, attitudes and behaviours in rural and periurban Kenya. This manuscript presents the protocol of the Afya Kesho programme. The study employs a quasiexperimental pre-post design to assess the effectiveness of the programme.