Children’s sedentary time has increased, while daily physical activity and motor performance have decreased. We evaluated an integrated school-based exercise program by assessing changes in motor skills after one year and comparing these changes to children who did not participate. We included 303 children from five schools in this longitudinal study and assigned them either to the exercise group (EG; n = 183 with daily exercise program) or the waiting group (WG; n = 120). Motor skills were assessed at baseline and after one year. Mixed modeling was used to analyze inter-group differences of change in motor skills and to determine the effect of sex, age group, and weight status. EG improved more strongly than WG for sprint, side jumps (both p = 0.017), stand and reach (p = 0.012), and ergometry (p ≤ 0.001) when compared to WG. Girls improved more strongly in the sit-ups than boys, second graders more than fifth graders in the backwards balance and the ergometry, and non-overweight children more in the standing long jump than overweight children. The exercise program is effective in increasing motor skills and physical fitness. Girls were not disadvantaged, and overweight children profited as much as their non-overweight peers in all categories but one.