Purpose The effects of aerobic exercise on bone metabolism are still unclear. Thus, the main goal of this study was to explore if there was an effect of the short-term aerobic exercise program on the bone remodeling process and if there were sex differences in the effect of the training program on bone metabolism. Methods Twenty-one participants (men and women) aged 20–23 performed an 8-week aerobic exercise program three times per week in 1-h sessions with increases in the exercise load every 2 weeks. Bone density, bone mineral content and concentration of markers of bone metabolism: osteocalcin, C-terminal procollagen type I peptide, pyridinoline, parathyroid hormone, osteoprotegerin, and the receptor activator of nuclear kappa B ligand by ELISA were measured at the start and at the end of the study, while changes in body composition were assessed by a bioelectric impedance analysis method 6 times during the study. Results The aerobic exercise program increased the concentration of osteocalcin (11.34 vs 14.24 ng/ml), pyridinoline (67.51 vs 73.99 nmol/l), and the receptor activator of nuclear kappa B ligand (95.122 vs 158.15 pg/ml). A statistically significant increase in bone density at neck mean (1.122 vs 1.176 g/cm 3 ) and in bone mineral content at dual femur (33.485 vs 33.700 g) was found in women, while there was no statistically significant change at any site in men. Conclusion 8 weeks of the aerobic exercise program with increment in intensity increased some of bone remodeling biomarkers and showed different effects for men and women.