BACKGROUND: Physical activity at school can support obesity prevention among youth. This paper assesses the role of existing school physical activity programs for a national cohort from first grade to fifth grade. METHODS: We analyzed a cohort from the Early Childhood Longitudinal Survey—Kindergarten Cohort which included 8246 children in 970 schools across the country. Growth curve models estimate the effect of physical education (PE) and recess on individual child body mass trajectories controlling for child and school characteristics. Hierarchical models allow for unobserved school and child effects. RESULTS: Among first graders, 7.0% met the National Association of Sport and Physical Education (NASPE) recommended time for PE and 70.7% met the recommended time for recess in the previous week. Boys experienced a greater increase in body mass than girls. Meeting the NASPE recommended time for recess was associated with a 0.74 unit decrease in BMI (body mass index) percentile for children overall. Meeting the NASPE recommendation for physical education was associated with 1.56 unit decrease in BMI percentile among boys but not girls. CONCLUSIONS: We find evidence that meeting the national recommendations for PE and recess is effective in mitigating body mass increase among children.