Background: The comprehensive school health (CSH) framework has four components: social and physical environment; partnerships and services; teaching and learning; and policy. This study examines associations between CSH and student physical activity (PA). Methods: Using 2015/2016 COMPASS study survey data of 37,397 students (grades 9-12) from 80 secondary schools in Ontario and Alberta, Canada, associations between school-level factors within CSH and student PA outcomes (weekly moderate-to-vigorous PA [MVPA] minutes and achieving the national PA recommendations of [greater than or equal to]60 min of MVPA daily, vigorous PA [greater than or equal to]3 days/week, strengthening activities [greater than or equal to]3 days/week) were analyzed using multilevel regression models stratified by gender and grade. Results: Factors within all four CSH components were associated with student PA. Four student subgroups were more likely to achieve the recommendations if their school had youth organization partnerships (Range of AORs:1.15-1.33, p <0.05) and female students were less likely if their school had low prioritization of PA (AOR = 0.77, 95% CI: [0.65-0.92]). Grade 9 students had higher MVPA when provided non-competitive PA opportunities ([beta] = 100.4, 95%CI: [30.0-170.9]). All student subgroups had better PA outcomes when schools provided access to equipment during non-instructional time. Conclusion: There is opportunity to improve student PA through CSH-guided interventions, but different strategies may be more effective for each gender/grade.