Objectives: Single sex after-school physical activity programs show potential to prevent unhealthy weight gain. The aim of this study was to assess the acceptability and potential efficacy of single-sex after-school physical activity programs for overweight and at-risk children from low-income communities. Design: 7-month, 2-arm parallel-group, RCT, conducted at an elementary school in a disadvantaged area in Wollongong, Australia (March-November 2010). Methods: 20 boys and 17 girls were randomized to intervention (PA) or active comparison groups (HL). Primary outcomes included implementation, acceptability, percentage body fat and BMI z-score. Results: The PA programs were acceptable with high implementation and enjoyment rates. At 7 months postintervention girls in the PA group displayed greater changes in percentage body fat (adjust diff. = -1.70, [95% CI -3.25, -0.14]; d = -0.83) and BMI z-score (-0.19 [-0.36, -0.03]; d= -1.00). At 7 months boys in the PA group showed greater changes in waist circumference (-3.87 cm [-7.80, 0.15]; d= -0.90) and waist circumference z-score (-0.33 [-0.64, -0.03]; d= -0.98). For both boys' and girls' PA groups, changes in adiposity were not maintained at 12-month follow-up. Conclusions: Single-sex after-school physical activity programs are acceptable and potentially efficacious in preventing unhealthy weight gain among overweight and at-risk children. However improvements are hard to sustain once programs finish operating.