The global prevalence of childhood obesity is high. Obesity main causes are linked to sedentary lifestyles. Increasing physical activity (PA) and reducing sedentary activities are recommended to prevent and treat obesity. This study aimed to evaluate the effectiveness of a 6-month school PA intervention on obesity prevention and healthy behaviors in school-aged children. Participating students (10-11 years of age) were randomly divided into an intervention group and a control group. Children in the intervention group (n = 80) participated in a multicomponent PA that included improvement in extracurricular physical activities (with an additional 40 min per day for 5/6 days per week). Children (n = 80) in the control group participated in usual practice. Participants had mean body mass index of 19.7 ± 2.9 kg/m2 , and 33.7% of them were overweight or with obesity at T0. The change in body mass index in intervention group (-2.4 ± 0.6 kg/m2 ) was significantly different from that in control group (3.01 ± 1.8 kg/m2 ). The effects on waist circumference, waist-to-height ratio, and physic fitness were also significant in intervention group compared with control group (all p < 0.05). Furthermore, there is a significant decrease in overweight or children with obesity in the experimental group (to 17.5%, p < 0.05). These findings suggest that a school-based intervention program represents an effective strategy for decreasing the number of overweight and children with obesity.