School food and physical activity (PA) environments can influence children’s dietary and physical activity behaviors. However, evidence on whether school environment is associated with students’ weight status is less definitive. In this study, we examined the association between students’ body mass index (BMI) and measures of school food and PA environments. We calculated BMI from nurse-measured data collected on 19,188 6–19-year-old students from 90 public schools in four low-income cities in New Jersey in 2015–2016. Based on a questionnaire administered to school nurses, we constructed 6 food and 3 PA indices capturing the healthfulness of key dimensions in the school food and PA environment domains. Multilevel linear models, stratified by school level (elementary and secondary), examined the association between BMI z-scores and indices of the school environment. The food and PA domains were modeled separately and then combined. Joint significance of indices within each domain was tested. Analyses were conducted in 2019–2020. In the combined model for elementary schools, indices in both the food and PA domains were jointly significant (p = 0.005 and p < 0.001, respectively). With regard to specific indices in the model, students’ BMI z-score was 0.03 units lower for each additional outdoor PA facility (95% CI [−0.06, −0.00]; p = 0.036). Similarly, for secondary schools, both the food and PA domains were jointly significant (p = 0.004 and p = 0.020, respectively). Each additional unhealthy item in vending machines was associated with a 0.12 unit increase in BMI z-score (95% CI [+0.00, 0.23]; p = 0.042). Overall, healthier food and PA environments were associated with lower student BMI.