This study aimed to investigate the effect of vitamin D3 supplementation at a dose of 4,000 IU/day for 6 weeks on serum levels of: 25-hydroxyvitamin D [25(OH)D], bone turnover [osteocalcin and carboxy-terminal telopeptides of crosslinks of type I collagen (CTx-I)], and muscle damage [lactate dehydrogenase (LDH) and creatine kinase (CK)] in middle adolescent (15-18 years) and late-adolescent to early adulthood (19-30 years) female basketball players with inadequate vitamin D status. Participants (N=24) were randomly assigned in a double-blind manner into a vitamin D or placebo group. Data were analyzed using separate 2×2x2 mixed ANOVAs with one within-subjects factor (time) and two between-subjects factors (condition and age). When a significant interaction was observed, the intra-group changes were assessed using paired t tests and Hedge's g. Paired t-tests comparing intra-group changes in the vitamin D condition revealed a non-significant large improvement in 25(OH)D (p = 0.06; g = 0.86), non-significant small decreases in CTx-I (p = 0.13; g = −0.22) and CK (p = 0.07; g = −0.26), as well as a significant moderate decrease in LDH (p = 0.004; g = −0.74). Paired t-tests comparing intra-group changes in the placebo condition revealed a significant moderate decline in 25(OH)D (p <0.001; g = −0.77), as well as significant small increases in CTx-I (p = 0.04; g = 0.47) and CK (p = 0.04; g = 0.36). Vitamin D3 supplementation at 4,000 IU/day could be effective in reducing bone resorption and muscle damage in female basketball players with inadequate baseline vitamin D, irrespective of age.