Background: The school environment has the potential to influence student body mass index (BMI) through programs and policies. Our objective was to examine the effect of modifying obesity-related school policies and programs on youths' BMI trajectories. Methods: Obesity-related school policies and programs related to physical activity and healthy eating were collected from 41 schools across Ontario at baseline (2012-2013) and year 2 (2013-2014) of the COMPASS study. Self-reported height and weight were collected from the 4951 grades 9 and 10 students who attended those schools for 3 years. Linear mixed effects regression models examined the effect of modifying obesity-related school policies and programs on youths' BMI trajectories. Results: Between Y[subscript 1] and Y[subscript 2], 26 of the 41 schools implemented distinct new obesity-related programs or policies related to physical activity or healthy eating. Five of the interventions were associated with BMI trajectories of students attending those schools compared to students attending a pooled sample of control schools, predicting a higher BMI trajectory. Conclusions: Isolated programs and policies may not successfully improve youths' BMI trajectories. Further research is required to test the implementation of policies and programs that follow a comprehensive school health (CSH) approach, targeting BMI and associated behaviors.