The female athlete triad is a syndrome that leads to disordered eating, amenorrhea, and osteoporosis. The pathophysiologic mechanisms that lead to reduced bone mass in female athletes are low energy and functional hypothalamic amenorrhea. The aim of the present study was to establish an animal model of osteoporosis, which is similar to the osteoporosis seen in female athletes. We investigated the effects of long-term energy restriction on bone mineral density (BMD), and the levels of 17β-estradiol (E₂) and luteinizing hormone (LH) in voluntary wheel-running female rats. Fourteen female Sprague-Dawley rats (8 weeks old) were randomly categorized into 2 groups: running (RUN) group and sedentary (SED) group. At 18 weeks of age, the rats in the RUN group were further randomly divided into 2 groups: running-ad libitum feeding group (RC group) or running-restricted feeding group (RR group). Twenty-four weeks after the experimental period, the RR group showed significantly lower BMD and plasma LH levels than the RC and SED groups (p < 0.05). Plasma E₂ levels in the RR group were significantly lower than that in the SED group (p < 0.05). The present study indicated that long-term energy restriction with voluntary wheel running exhibited low bone mass in female rats with intact ovaries. Furthermore, the distinct endocrine profiles observed in this model suggest that energy restriction with voluntary exercise disturbs the hypothalamic-pituitary-ovarian axis. This may establish a model for the development of osteoporosis in the exercising human female with energy restriction, caused by dysfunction of the reproductive system.