The objectives of this study were to derive trajectories of childhood participation in organized physical activity (PA) and to examine how these trajectories are associated with pre-existing and subsequent emotional adjustment. Trajectories of mother-reported participation in organized PA were derived from age 6 to 10 for 1492 children from the Québec Longitudinal Study of Child Development birth cohort. Parents and teachers reported on internalizing behavior (emotional distress, anxiety, shyness, social withdrawal) at ages 4 and 12, respectively. Longitudinal latent class analysis identified two typical trajectories of participation in organized PA. The Consistent Participation trajectory (61%) included children with elevated probability of participation at all ages. The Low-Inconsistent Participation trajectory (39%) included children who did not participate or participated only once or twice, generally in late childhood. Pre-existing internalizing behavior at age 4 did not predict trajectory membership. However, children in the Low-Inconsistent Participation trajectory showed higher subsequent emotional distress (B = 0.87, 95% confidence interval [CI] = 0.46-1.28), anxiety (B = 0.61, 95% CI = 0.18-1.04), shyness (B = 0.92, 95% CI = 0.39-1.44), and social withdrawal (B = 0.86, 95% CI = 0.37-1.34) at age 12 than those in the Consistent Participation trajectory. Our findings suggest that early and sustained involvement in organized PA is beneficial for children's emotional development.