Background: For rural adolescents, schools are among the few places where environmental interventions can promote health outside of the home. The goal of this study was to assess the nutrition and physical activity (N&PA) environments of schools attended by a birth cohort and examine the association with change in body mass index (BMI) from sixth to eighth grade. Methods: Using data from adolescents of a rural New York State birth cohort (N?=?281), we used linear mixed models to identify N&PA environments associated with change in BMI. We also examined family income trajectory as a potential modifier to consider how the association between school environment and change in BMI might differ depending on income. Results: We found considerable heterogeneity in environments within and between schools. Among students with low-income trajectories, reductions in BMI z-scores were associated with school environments that promote better physical education (PE) and general (non-PE, non-sport) physical activity. Schools with better sports environments were associated with reductions in BMI for some students, but not lower-income students. Conclusions: School environments may have differing effects on students depending on their socioeconomic status. Strategies are needed to identify and address barriers that impair low-income students' access to health-promoting school resources.