In Malawi, secondary schools often lack adequate physical activity opportunities despite evidence suggesting their importance for academic performance. A mixed-method comparative study involving quantitative analysis of standardised test scores and qualitative interviews with teachers and students from randomly selected schools. Schools implementing physical activity programmes showed a 15% improvement in average test scores compared to non-participating schools, with themes indicating increased student engagement and teacher support for such initiatives. Physical activity programmes can significantly enhance academic performance in Malawian secondary schools. Schools should integrate physical activity into their curricula and provide necessary resources, while policymakers should promote these initiatives as a means to improve educational outcomes.