Purpose: To investigate the effect of an obstacle course based physical education program, designed according to contemporary insights on motor learning, on motor competence (MC) of 6- to 7-year-old Flemish children. Method: Pupils from 16 primary schools were randomly allocated to either control (n = 173, 50.3% boys) or intervention group (n = 182, 54.9% boys). MC, assessed with the Körperkoordinationtest für Kinder (KTK), was analyzed with a 2 (Gender, girls vs. boys) x 2 (Group: INT vs. CON) x 3 (Time: pre vs. inter vs. post) Repeated Measures ANOVA. Results: The MC in the intervention group improved more compared with the control group (Time x Group interaction, p < 0.001). Moreover, a shift to a more favorable MC classification is seen for all children in intervention group. Conclusion: The results underline the potential value of an obstacle course based PE program based and provide a gateway for optimization of the current PE programs.