(1) Background: Overweight children usually have lower levels of physical activity (PA) than their normal-weight peers. Low PA predisposes to an increase in body fat mass. The aim of this study was to evaluate the effectiveness of school-based PA intervention on the anthropometric indicators and body composition of overweight and obese children during a two-year observation period, from the age of 10 to 12. (2) Materials and methods: The research included 148 children with overweight or obesity who were born in 2007. There were two groups of children with standard and elevated PA at school (SPA and EPA; 4 and 10 h of physical education lessons a week, respectively). Anthropometric and body composition measurements were carried out. Body mass index (BMI), fat mass (FM), fat-free mass (FFM), skeletal muscle mass (SMM), and total body water (TBW) were estimated. In total, five measurements were conducted at intervals of 5–6 months. (3) Results: In EPA group, the percentage of obese children decreased from 46% to 35.25%, and in SPA group, this percentage increased from 42.75% to 46%. Only 3.33% of children in the standard PA group (one child) and 17.2% in the elevated PA group (six children) changed their BMI and FM categories from overweight to normal body mass. In EPA children, FM decreased from 28.65% to 26.41%, and in SPA children, it increased from 30.31% to 31.75%. The highest increase in FFM was in EPA boys, while SPA boys recorded the highest decrease. In SPA children, SMM increased by 0.43% from 38.85% to 39.28%, and in EPA children, it increased by 2.51% from 40.27% to 42.78%. In EPA children, TBW slightly increased from 53.26% to 53.59%, and in SPA children, it decreased from 50.70% to 49.93%. (4) Conclusions: Elevated PA at school has a positive effect on the BMI and body composition of children who are overweight or obese. Increasing the mandatory number of physical education lessons in school curricula is an efficient strategy for reducing obesity in school-aged children.