Inadequate dietary intake and prolonged amenorrhea in women athletes can lead to bone loss, particularly at the spine, which may be irreversible. This report presents the case of a woman endurance runner, followed prospectively over 6 years after presenting with the female athlete triad. Bone mineral density (BMD) and body composition were assessed by dual-energy X-ray absorptiometry. At baseline, lumbar spine (LS), total hip and total body (TB) BMD Z-scores were -2.2, -0.5 and -0.3 respectively. At 6 years, following a recovery plan of cognitive behavioural therapy (CBT), weight gain, improved dietary intake and reduced training load, the athlete regained menstrual function and BMD. LS, TB and hip BMD Z-scores improved to -0.6, -0.1 and 0.1 respectively. Restoration of fertility was indicated by pregnancy, following only 4 months of regular menstruation. This case report suggests that bone density and fertility may not be completely jeopardised in formerly amenorrheic and osteopenic athletes, providing recovery through diet, weight gain, and return of menstruation is achieved within the third decade. Longitudinal studies tracking bone changes in women with amenorrhea and low BMD are required and would have important implications for the treatment of the female athlete triad.