Background: The aim of this study was to examine the efficacy of an embedded after-school intervention, on promoting physical activity and academic achievement in primary-school-aged children. Methods: This 6-month, 2-arm cluster randomized controlled trial involved 4 after-school centers. Two centers were randomly assigned to the intervention, which involved training the center staff on and implementing structured physical activity (team sports and physical activity sessions for 75 min) and academic enrichment activities (45 min). The activities were implemented 3 afternoons per week for 2.5 hours. The control centers continued their usual after-school care practice. After-school physical activity (accelerometry) and executive functions (working memory, inhibition, and cognitive flexibility) were assessed pre- and postintervention. Results: A total of 60 children were assessed (7.7 [1.8] y; 50% girls) preintervention and postintervention (77% retention rate). Children in the intervention centers spent significantly more time in moderate to vigorous physical activity (adjusted difference = 2.4%; 95% confidence interval, 0.6 to 4.2; P = .026) and scored higher on cognitive flexibility (adjusted difference = 1.9 units; 95% confidence interval, 0.9 to 3.0; P = .009). About 92% of the intervention sessions were implemented. The participation rates varied between 51% and 94%. Conclusion: This after-school intervention was successful at increasing moderate to vigorous physical activity and enhancing cognitive flexibility in children. As the intervention was implemented by the center staff and local university students, further testing for effectiveness and scalability in a larger trial is required.