The ratio of the anti-Müllerian hormone (AMH) precursor (proAMH) to active AMH (AMHN,C) is higher in childhood than in adulthood but has never been quantified during adolescence. The ratio of proAMH to total AMH (AMH prohormone index, API) was examined during the puberty in healthy girls. The API was also compared between girls with and without polycystic ovary syndrome (PCOS) to determine if there were differences that could assist in PCOS diagnosis during adolescence. Total AMH and proAMH were measured by immunoassay in a single-centre, cross-sectional observational study; 61 controls and 29 girls with PCOS were included in the study (age range 8-21 years). The API was calculated as proAMH as a percentage of total AMH. Differences in API between control and PCOS subjects and across age-groups were examined by Welch's ANOVA. The relationship between API and a range of metabolic parameters was examined by Pearson correlation. The API in healthy females increased between the ages of 10~15 years and declined from 15~20 years (p < 0.001). The API was negatively correlated with body mass index in the control (p = 0.04) and PCOS groups (p = 0.007). The API was associated with factors related to adiposity and lipid metabolism. The API was not significantly different in control girls and girls with PCOS. Higher API during adolescence suggests that proteolytic activation of proAMH is suppressed during this life stage. API was not different between control girls and girls with PCOS indicating that it is not useful in diagnosis of PCOS during adolescence.