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Introduction: Many adolescents in low- and middle-income countries face challenges related to sexual and reproductive health and rights, which are exacerbated by gender inequalities. One approach to address these issues is the integration of Comprehensive Sexuality Education (CSE) in schools. However, the process of effectively implementing CSE in these settings is often suboptimal. There is a significant lack of research exploring the specific conditions and methods that effectively lead to enhanced knowledge and improved decision-making in sexuality and gender equality among adolescents through CSE. This realist evaluation protocol will address this gap by exploring how the nature and pattern through which CSE is provided has a) changed adolescents’ knowledge regarding sexuality and gender relations and b) shaped adolescents’ capacity to make positive decisions.

Methods: This study uses a multiple-case design, combining realist evaluation with participatory action research methods to explore Comprehensive Sexuality Education (CSE) integration across multiple levels in Eastern province—from provincial to community levels. Data collection will occur in phases, utilizing interviews, photovoice, drawings, reviews, and observations. The study involves several key steps: 1) identifying challenges to CSE integration, 2) creating an initial theory or action plan that explains how CSE promotes positive decisions among adolescents about sexuality, 3) testing this theory through case studies, and 4) refining the theory and formulating recommendations to improve future CSE integration. Additionally, the study will document informal, contextual, and horizontal factors (ICAMO configurations) that influence the integration of CSE at the school level and affect adolescents' understanding and decision-making regarding sexuality and gender relations.

Discussion: This study will contribute to the development of strategies for effectively facilitating the integration process of similar programmes within the school system. The study will further contribute to methodological development in participatory research driven realist evaluation.