This study tested whether overweight/obese children’s attendance in a community-based physical activity (PA) program was associated with changes in cardiorespiratory fitness (CRF) and adiposity and whether in-program activity levels influenced those associations. Program sessions (offered twice/week, 2 hours/session, over 9 months) included structured exercise/sports. At baseline and follow-up, CRF was measured as Progressive Aerobic Cardiorespiratory Endurance Run (PACER) laps, height/weight were measured, and body mass index (BMI) was calculated. Attendance was recorded as sessions attended. Children wore pedometers in 10 representative sessions; in-program activity was calculated as mean steps/minute across sessions. Linear mixed models tested associations between attendance and changes in PACER score and BMI and the influence of in-program activity on those associations. A total of 101 participants (56% male, 93% Hispanic) completed baseline and one or two follow-up fitness/adiposity measurements. Attendance was associated with PACER change (β = .093, p = .01) but not BMI change (β = .00026, p = .97). There were significant interactions between attendance and in-program activity: Attendance more favorably affected PACER (p < .0001) and BMI (p = .03) as in-program activity levels increased. Attending community-based PA programs may improve CRF among overweight/obese children, particularly when participants are highly active during program time. Community practitioners should not only enroll overweight/obese children in PA programs but also promote adequate attendance/in-program activity levels.