This study investigated the effect of integrating music into physical activity on Basic Six pupils’ cognitive, affective, and psychomotor development in Winneba, Ghana. A single-group pre-test post-test quasi-experimental design was used, involving 28 pupils (14 males, 14 females) purposively selected from the University Practice School. The intervention consisted of two 60-minute sessions weekly for six weeks, incorporating structured physical activities with popular music. Cognitive and affective domains were assessed using a questionnaire, while psychomotor skills were evaluated through flexibility, cardiovascular endurance, and strength tests conducted at pre-and post-test stages. Findings revealed significant improvements in cognitive (t(27) = 9.74, p < .001) and affective (t(27) = 9.73, p < .001) domains and aerobic capacity (t(27) = 6.09, p < .001) except flexibility which showed no significant change (t(27) = 0.29, p = .777). These results suggest that integrating music into physical education enhances the holistic development of learners by fostering their cognitive engagement, emotional well-being, and physical fitness. We recommend that physical education lessons should be taught with music especially in primary schools for the holistic development of children as well as to sustain their interest in regular participation in physical activity for lifelong and healthy living.