Purpose: Children’s sedentary time has increased in recent years, especially during school, while daily physical activity has decreased. The lack of physical activity can contribute to a deterioration in motor performance, which is key to a healthy development. We implemented a comprehensive exercise program in the school setting. Our study aimed to evaluate this program by assessing changes in motor skills after one year and to compare these changes to children who did not participate.Methods: A total of 357 children from 5 schools were included in this observational longitudinal cohort study. Motor skills were assessed using the German Motor Test 6-18. Children were either assigned to the exercise group (EG) or waiting group (WG). The EG participated in the physical activity program for one year. Of those, a total of 303 children (EG n=183; WG n=120) completed motor tests at baseline and follow-up one year later, and comprise the study population. Linear mixed modeling was used to calculate corrected means and analyze for inter-group differences of change in motor skills after one year between the groups, and to determine the effect of sex, age group and weight category on the change in motor skills. Results: After one year of additional physical activity, the EG improved significantly more strongly in 6 out of 8 motor skill tests than the WG. After the adjustment for sex, age, and BMI the improvement is still significantly stronger in the EG in 4 of 8 motor skill tests (sprint, side jumps, both p=0.017; stand and reach, p=0.012; ergometry, p=<0.001), when compared to the WG. Girls improved more strongly in the sit-ups than boys, 2nd graders more than 5th graders in the backwards balance and the ergometry, non-overweight pupils more in the standing long jump than overweight children. Conclusions: Participating in the exercise program for one year positively influenced motor skill development in schoolchildren. Our data suggest that girls were not disadvantaged, and even improved more than boys in the sit-ups, and that overweight pupils profited as much as their non-overweight peers in all categories but one. The exercise program, simple and easily implemented into the school routine, is effective in increasing motor skills and physical fitness.