Objectives The aim of this study was to investigate the effect of a 20-week exercise program on bone mineral parameters in children with overweight or obesity. Design Randomized controlled trial. Methods This study took part from November 21, 2014, to June 30, 2016, in Granada, Spain. A secondary analysis of this parallel-group randomized controlled trial was performed with 77 children with overweight or obesity (9.9 ± 1.2, 65 % boys) who were randomly allocated to exercise or control group. All participants received lifestyle recommendations. The control group continued their usual routines, whereas the exercise group attended a minimum of 3 supervised 90-min sessions/week of aerobic plus resistance training for 20 weeks. A whole-body scan by dual-energy x-ray absorptiometry was carried out to obtain body composition at total body less head, arms, lumbar spine, pelvis, and legs. Results Participants in the exercise group acquired significantly higher total body aBMD (mean z-score [95 % confidence intervals, CI], 0.607 [0.522–0.692]) compared with the participants in the control group (mean z-score, 0.472 [0.388–0.556]); difference between groups, 0.135 standard deviations [95 % CI 0.015–0.255], and legs aBMD (mean z-score, 0.629 [0.550 to 0.708]); control group (mean z-score, 0.518 [0.440 to 0.596]); difference between groups, 0.111 [0.001 to 0.222]; all p < 0.05. There were no significant differences between exercise group and control group at the remaining evaluated regions (p > 0.05). Conclusion A 20-week non-specifically bone-targeted exercise program induced a small, yet significant, improvement on total body and legs aBMD in children with overweight or obesity. Future studies should investigate the interaction of weight status in the bone response to exercise programs.