Juvenile obesity is increasing worldwide. Preventive strategies are warranted. The school-based Children's Health Interventional Trial (the CHILT Project) combines health education and physical activity for children. The effect on obesity and physical performance was studied after four years in 12 primary schools compared with five control schools. Anthropometric data were recorded. Physical performance was measured by a coordination test for children (balancing backwards, one-legged obstacle jumping, lateral jumping, sideways movements) and a 6-min run (endurance). No difference in the prevalence and incidence of overweight and obesity was found between the intervention and control schools before and after the intervention. Remission of overweight was higher in the intervention schools (23.2 vs. 19.2%), but not significant. An increase in coordination related to lateral jumping and balancing backwards was apparent in the intervention schools (30.6, s = 10.8 vs. 26.1, s = 10.8, P = 0.005; 21.8, s = 11.8 vs. 19.4, s = 11.7, P = 0.007), and the increase in endurance performance tended to be higher in intervention schools (100.8, s = 122.7 vs. 92.8, s = 126.0, P = 0.055), adjusted for age, sex, baseline test result, and body mass index at final examination. Therefore, preventive intervention in primary school offers the possibility to improve physical performance in children. The prevalence and incidence of obesity were not affected.