Gender-specific physical education programmes (GPEPs) have been introduced in Nigerian secondary schools with the aim of addressing gender disparities and improving educational outcomes. However, their effectiveness is less understood compared to traditional models. This study will employ a qualitative comparative approach, synthesising existing literature on both GPEPs and TPEPs to develop a theoretical framework. The analysis will draw from educational research methodologies to evaluate the potential advantages of gender-specific interventions. This theoretical framework underscores the need for empirical research to validate these hypotheses and provide evidence-based recommendations for policymakers and educators. Policymakers should consider gender-specific interventions as part of a comprehensive physical education strategy, while also ensuring fair resource allocation to support all students.