The obesity epidemic and the decline of fitness among children highlights the need for suitable interventions designed to promote Physical Activity (PA) and healthy habits. The purpose of our pilot study was to assess the feasibility of a school-based program among overweight and obese children, by examining changes in their body composition, PA, physical fitness, and some psychosocial determinants of active behavior. An additional objective was to investigate the reciprocal relationship over time between PA and body image. Self-reported PA and health-related fitness tests were administered to 18 overweight and obese children (11.3 ± 0.4 years), before and after a 6-month intervention including nutritional education, skill-learning, playful physical activities, and exercise training. Participants were assessed on body composition, perceived physical ability, body image, and pleasant and unpleasant psychobiosocial states towards PA. After treatment, children showed decreased body mass index, body fat percentage, arm and waist circumferences, and skinfold thickness. Actual and perceived physical abilities, body image, and PA also improved over six months. Cross-lagged correlations suggest body image to be an antecedent to being physically active. Results showed that the multi-component school program may have sustainable benefits in reducing adiposity indicators and improving exercise adherence, physical fitness, and psychological well-being.