Background: Comprehensive school physical activity programming (CSPAP) has been shown to increase school day physical activity and health-related fitness. The use of goal setting may further enhance the outcomes of CSPAP. Purpose: The purpose of this study was to examine the effect of physical activity leader (PAL) goal setting on school day physical activity and cardiorespiratory endurance in low-income children from schools receiving CSPAP. Methods: Participants were 1704 children (mean age = 9.3 ± 1.6 years) recruited from 5 low-income elementary schools. The schools were stratified into schools where PALs employed goal-setting strategies and no goal-setting strategies. Schoolday step counts and progressive aerobic cardiovascular endurance run (PACER) laps were collected before CSPAP and after 36 weeks. Results: Sixth-graders who received goal setting displayed greater increases in school day step counts (? = 665 steps, P < 0.001, Cohen's d = 0.38) and PACER laps (? = 23.5 laps, P < 0.001, Cohen's d = 0.72) compared to children who did not receive goal setting. Discussion: The use of goal setting by school PALs led to greater improvements in physical activity and cardiorespiratory endurance in sixth-graders. Translation to Health Education Practice: Because physical activity and health-related fitness tend to decline as children transition into adolescence, the use of goal setting within school physical activity programming may attenuate these declines.