In this randomized pilot study, we examined the effects of yoga intervention on axial and peripheral bone mineral density (BMD), disordered eating cognitions, anxiety, and depression in adolescent girls with anorexia nervosa (AN). Fifteen young women aged 13-18 years with AN or atypical AN were randomized to either a Yoga group (n = 7), including twice-weekly yoga for 24 weeks plus standard outpatient care, or Non-Yoga group (n = 8), who received standard outpatient care alone. Data from anthropometrics, mental health and eating behavior questionnaires, dual-energy x-ray absorptiometry, and peripheral quantitative computed tomography measurements were obtained at baseline and 6 months. The adjunct of yoga to standard treatment resulted in statistically significant improvement of axial BMD, depression, and disordered eating cognitions in comparison to the Non-Yoga group. In conclusion, a gentle yoga intervention may be beneficial for improving bone and mental health in adolescent females with AN.