Background: Preventing overweight and improving physical fitness in primary school children is a worldwide challenge, and physically active intervention programs usually come with the cost of academic instruction time. This study aimed to investigate effects of physically active academic lessons on body mass index (BMI) and physical fitness in primary school children. Methods: Dutch children attending second- or third-grade class from 12 primary schools (N = 376; 8.1 ± 0.7 years) were randomly assigned to a 22-week intervention program or to the control group. In addition to measuring BMI before and after the intervention, physical fitness was measured with 5 items of the Eurofit test battery, measuring cardiovascular and muscular fitness. Results: Multilevel analysis showed a significant interaction effect between condition (intervention vs control) and grade (B = -0.47; p < 0.05). For third-grade children, BMI of the intervention group did not change significantly during the intervention period, whereas a significant increase was found in the control group. No significant main or interaction effects were found for cardiovascular or muscular fitness. Conclusions: The current physically active academic lessons had positive effects on BMI in third-grade children, but had no effects on cardiovascular and muscular fitness.