SummaryDisparities in physical activity and health outcomes exist between urban and rural youth. School settings can be utilized to promote physical activity in youth regardless of urban–rural status. This systematic review and meta‐analysis aimed to assess and compare the effect of rural and urban/suburban school‐based physical activity programs on total physical activity in youth. A search of five databases was conducted. A total of 33 studies remained after the exclusion process, 28 of which took place in urban/suburban schools and five of which took place in rural schools. The DerSimonian and Laird random effects model was employed with the estimates of heterogeneity taken from the inverse‐variance fixed‐effect model. For rural studies, the Hartung–Knapp–Sidak–Jonkman method was used to obtain error estimates. Results from the total sample indicated a significant but small pooled increase in daily physical activity (Hedge's g = 0.12, 95% confidence interval [CI]: 0.06–0.18), which held for interventions conducted in urban/suburban schools (Hedge's g = 0.12, 95% CI: 0.06–0.19). For rural school‐based interventions, there was no significant pooled effect (Hedge's g = 0.06, 95% CI: −0.50 to 0.61). This meta‐analysis provides evidence that school‐based interventions can be marginally effective for increasing daily physical activity in children and adolescents; however, no effect was observed for interventions implemented in rural settings.