Few studies have investigated the impact of school-based physical activity interventions on anthropometric characteristics concomitantly with aerobic and anaerobic capacities in young children. The present study aimed to assess the effect of a 6-month physical activity program on body composition and physical fitness among primary schoolchildren. Four hundred fifty-seven children aged 6 to 10 years were randomly assigned to the intervention group (229 children) or observational group (228 children). Participants' height and weight were assessed, and obesity was determined using French reference curves for BMI. The sum of the four skinfolds and fat-free mass were determined. Ground tests were used to assess aerobic (20-m shuttle run test) and anaerobic (cycling peak power) fitness before and after a 6-month physical activity intervention. The anthropometric modifications obtained over the 6 months cannot be attributed to the intervention as the ANOVA revealed no group effect (intervention vs. group). However, anaerobic and aerobic fitness were significantly improved, thanks to the program in both lean and obese children. A 6-month school-based physical activity intervention in 6- to 10-year-old children did not yield positive anthropometric improvements, but appears effective in terms of aerobic and anaerobic physical fitness. Two physical activity sessions per week in addition to standard physical education classes in primary schoolchildren bring effective results for the prevention of childhood obesity.