Background: Several studies have reported that prebiotics are beneficial in improving bone health due to their balancing effect on the gut microbiota. As numerous Japanese female athletes have issues related to bone health, a better understanding of the bioactivity of prebiotics are essential. The present study aimed to attempt continuous intake of prebiotic food would balance the gut microbiota, resulting in improved bone metabolism turnover marker among the Japanese female athletes.Methods: The participants included 29 female athletes aged 18–25 years. They were requested to consume their habitual foods or drinks with one pack of prebiotic food every day for 12 weeks. Dietary intake, energy expenditure, body composition, blood sample, and faecal gut microbiota was assessed during this intervention period.Results: Body composition, total energy intake, and total energy expenditure of the participants revealed no significant changes during the intervention period. The occupation ratio of Bifidobacterium spp. was significantly increased at 3 and 4 weeks (18.0% ± 8.3% and 17.6% ± 8.5%, respectively) compared to that of pre-intervention (11.7% ± 7.3%) (p = 0.019 and p = 0.035, respectively). Serum TRACP-5b level was significantly decreased at 12 weeks (363 ± 112 mU/dL) compared to that at baseline (430 ± 154 mU/dL) (p = 0.018).Conclusions: These results suggest that continued intake of inulin and lactulose fortified prebiotic food might have beneficial effects on bone health and gut microbial environment among the female athletes. Further studies are warranted to identify the mechanism of the prebiotics-gut-bone axis.Trial registration: Umin Clinical Trials Registry, UMIN000029589. Registered 17 October 2017.