This prospective controlled intervention study over 12 months evaluated the effect of exercise on muscular function, physical ability, and body composition in pre-pubertal boys. Sixty-eight boys aged 6–8 years, involved in a general school-based exercise program of 40 min per school day (200 min/week), were compared with 46 age-matched boys who participated in the general Swedish physical education curriculum of mean 60 min/week. Baseline and annual changes of body composition were measured by dual energy X-ray absorptiometry (DXA), stature, and body mass by standard equipments, isokinetic peak torque (PT) of the knee extensors, and flexors at 60 and 180 deg/sec by computerized dynamometer (Biodex) and vertical jump height (VJH) by a computerized electronic mat. The annual gain in stature and body mass was similar between the groups whereas the increase in total body and regional lean mass (P<.001) and fat mass (P<.001) was greater in the exercise group. The one-year gain in body mass-adjusted knee extensor and flexor PT at 180 deg/sec was significantly greater in the intervention group compared with the control group (P<.01, adjusted for age at baseline and P<.001, adjusted for age and muscle strength at baseline, resp.). There was no group difference in VJH. In conclusion, the increase in school-based physical education from 60 to 200 minutes per week enhances the development of lean body mass and muscle strength in pre-pubertal boys.