Inappropriately high weight in children is a persistent problem in the United States, and physical activity is often reduced in schools due to academic demands. Effective after-school programs could positively impact both physical activity and overweight/obesity, however previous reviews and meta-analyses have indicated minimal effects. Both 4- and 3-day/week versions of a social cognitive theory-driven physical activity/nutrition after-school program were evaluated against unstructured care to assess effects in children (overall M age = 10.00 years, SD =.80). For changes over 9 months in body mass index (BMI), effects sizes (Cohen's d) were.68,.40, and.07 in the 4-day (n = 70), 3-day (n = 70), and unstructured (n = 50) groups, respectively. Similar patterns of effects were found for changes in free-time physical activity and cardiovascular endurance. Incorporating a theory-based prediction model previously supported in teens through older adults, with and without medical disorders and health-risk factors, improvements in exercise-related self-regulation and self-efficacy, and mood, significantly predicted increased free-time physical activity (R 2 =.48). Effects significantly strengthened to R 2 =.62 when completion/non-completion of the recommended 300 min/week of physical activity was also accounted for. Change in BMI was inversely related to physical activity change, β=-.14, p <.05. The present evaluation process indicated promising effects, and indicated theory-based targets to foster future program improvements.