Purpose: The study aimed to test whether improvement in fitness components, mediates the changes in Health-related Quality of Life (HRQoL) after exercise intervention in overweight and obese children. Methods and design: 170 obese and overweight children (121 exercise group and 49 control group) participated in a public exercise program based on sports practice for 6 months, 2 h per week. Anthropometry, physical fitness, and HRQoL were measured. Magnitude-based inferences and Cohen's effect size were performed to analyze the program effect. To know which physical fitness components mediated the improvement on children's HRQoL, multiple mediation analyses were performed. Results: the analysis showed a moderate effect on some fitness components and a moderate and small effect on HRQoL. The improvement of agility or cardiorespiratory fitness showed a significant indirect effect on the enhancements in some HRQoL dimensions. Conclusion: after a 6-months exercise program in overweight and obese children, all physical fitness components improved, being responsible for the improvement of the HRQoL, agility and cardiorespiratory fitness.