Sports participation has potential to promote physical activity in youth. Unfortunately, sports participation and physical activity may decline from childhood to adolescence and into adulthood. Globally, only 20% of 13–15-year-olds meet the World Health Organisation recommendations for physical activity. This study aimed to investigate the 5-year trajectories of sports participation and their association with baseline motor performance in Danish school children as part of the Childhood Health Activity and Motor Performance School Study-Denmark (CHAMPS-DK), a school-based physical activity intervention study which investigated the health benefits of increased physical education lessons. Five distinct trajectories were identified, with group 1 maintained a stable trajectory of little to no sports participation, and group 2 showing a low decreasing trend. Group 3–5, the most sports active, demonstrated increasing sport participation at different rates. Baseline motor performance score was associated with the two most active sports participation groups. Students who were more physically active during school hours participated less in organised leisure time sports. This suggest focusing on improving motor performance in youth may support future sports participation and thus health-related physical activity. But also, that it might be necessary to engage and maintain children and adolescents in leisure time sports while implementing physical activity promotion interventions.