Aim We evaluated the effect that increasing physical education lessons from 1.5 to 4.5 hours per week for 5 years had on the body mass index (BMI) and waist circumferences of children aged 5‐11 years at inclusion. Methods From 2008 to 2013, six intervention schools in Svendborg, Denmark, delivered 4.5 hours of physical education lessons per week to 750 children. Meanwhile, four matched control schools gave 549 children the standard 1.5 hours of physical education lessons per week. Measurements were taken at baseline and yearly for 5 years. Of the 1299 children, 81 joined the schools after 2008. Results At baseline, the percentage of overweight children was 12% in the intervention schools and 13% in the control schools, whereas 15% and 19% were abdominal obese, respectively. After 5 years, the respective risks of remaining abdominal obese or overweight were 43% and 51% in the intervention schools and 78% and 84% in the control schools. Mean BMI increased 0.450 kg/m2 more in the control group over the five‐year period. The intervention was not effective in decreasing the average waist circumference. Conclusion Three times as much physical education lessons per week, for 5 years, effectively decreased BMI and the likelihood of remaining overweight or obese.