Background: The effectiveness of school-based physical activity interventions for improving cardiopulmonary fitness (CPF) of overweight and obese children is not well established. In this study, we evaluated whether overweight and obese children had similar changes in body mass index (BMI) and CPF as normal weight children after participating in a program for one academic year. Methods: Using purposive sampling at the school level, we selected 16 program and 7 control schools in a large metropolitan area in the Southeast during the 2015-2016 academic year. In these schools, 3396 fourth-graders participated with parental consent. Of these, 2332 (68.7%) participated in BMI measures and 1780 (52.4%) in Progressive Aerobic Cardiovascular Endurance Run (PACER) measures for CPF at two time points. Results: Students of all weight statuses pre-program did not show changes in BMI after program implementation. All students showed statistically significant improvements in the PACER test at follow-up, regardless of their participation in the program. However, overweight and obese children showed less improvement in CPF level than their normal weight classmates, regardless of their participation in the program. Conclusion: Special attention for improving engagements of overweight and obese children may be needed to achieve improvements in their CPF level similar to that of normal weight students.