To explore whether school poverty level and funding modified the effectiveness of an evidence-based Comprehensive School Physical Activity Program called Health Empowers You! implemented in elementary schools in Georgia. Secondary data analysis of a multi-level, cluster-randomized controlled trial. 40 elementary schools in Georgia in 2018-2019. 4th grade students in Georgia. Intervention schools implemented the Health Empowers You! program to increase school-day physical activity. The outcome was average daily moderate-to-vigorous physical activity, school free-reduced price lunch (FRPL) percentage and per pupil expenditures were effect modifiers. Separate linear mixed regression models estimated the effect of the intervention on average daily moderate-to-vigorous physical activity, with interaction terms between intervention status and (1) school FRPL percentage or (2) per pupil expenditures. The effect of the intervention was significantly higher in schools with higher FRPL percentage (intervention*school % FRPL β (95% CI): .06 (.01, .12)), and was modestly, but not statistically significantly, higher in schools with lower per pupil expenditures. Findings support the use of the Health Empowers You! intervention, which was effective in lower income schools, and may potentially reduce disparities in students' physical activity levels.