Our goal was to investigate the role of body mass index (BMI) and motor competence (MC) in children's physical activity (PA) levels during physical education (PE) classes. We assessed PA levels of 5-to-10-year old children ("n" = 264) with pedometers in four PE classes. MC was assessed using the TGMD-2 and BMI values were classified according to CDC guidelines. We found small-to-moderate positive correlations between MC and PA; BMI was not significantly correlated with MC and PA. The linear regression model indicated that overall MC was a better predictor of PA than BMI. Our results suggest that children with higher MC find a way to be more active even in a structured setting such as a PE class. Our findings draw attention to the importance of promoting MC, especially for children with high BMI. (Contains 2 tables.)