Objective: Several studies have reported anti-Müllerian hormone (AMH) concentrations in girls with polycystic ovarian syndrome (PCOS), but longitudinal studies of changes in AMH concentrations in relation to change in weight status are lacking in Indian adolescent girls with PCOS. Our objective was to study the longitudinal changes in AMH concentrations in obese Indian adolescent girls with PCOS with respect to weight loss. Materials and methods: This longitudinal study was conducted at the adolescent clinic of Shrikhande Hospital and Research Centre Pvt Limited, Nagpur, India, from January 2017 to December 2017. 120 obese girls aged 13-19 years (50% with PCOS) were included in the study after obtaining informed consent. Girls with and without PCOS were matched to age, BMI, and weight status. Serum AMH, gonadotropins, testosterone, and oestradiol levels were determined. The intervention consisted of promoting physical activity, delivering nutrition education, and behavior therapy. Normal distribution was tested by the Kolmogorov-Smirnov test for all variables. The primary outcome was the change in AMH concentrations over time. Results: Obese girls with PCOS demonstrated significantly (p < 0.001) higher AMH concentrations (5.7 ± 3.1 ng/mL) as compared to obese girls without PCOS (2.4 ± 1.3 ng/mL). Participants who had experienced weight loss were found to have significantly lower baseline AMH levels (−1.3 ± 1.8 ng/mL, p = 0.04). An association was also found between degree of weight loss and a decline in AMH levels, with subjects experiencing more weight loss demonstrating a higher decline in AMH level (−10.5 ± 1.1 kg vs −4.0 ± 1.0 kg; p = 0.001). Conclusion: Anti-Müllerian hormone was increased in Indian obese adolescent girls with PCOS and decreased with weight loss.