Background: Polycystic ovary syndrome (PCOS) affects 3–8% of adolescents. It is characterized by hyperandrogenism and oligoovulation/anovulation. PCOS has a negative impact on health-related quality of life (HRQoL). However, the extents to which factors influence total HRQoL of adolescents are not known. Adult PCOS patients have a higher incidence of binge eating than the general reproductive-age female population. Limited data on binge eating in adolescents with PCOS are available. Aim of this study was to investigate how PCOS and its associated factors, including binge eating, affect the HRQoL of adolescent girls. Methods: This case-control study recruited 63 adolescent girls 13–18 years of age with PCOS and 66 age-matched healthy controls. The PCOS health-related quality of life questionnaire (PCOSQ) and Binge Eating Scale (BES) were used. Multiple linear regression was executed to establish exact predictors and their effect on total HRQoL. Results: HRQoL was significantly lower in adolescents with PCOS than controls (4.9 (interquartile range (IQR) 1.5) vs. 5.8 (IQR 0.9) points). The lowest scores were found in the body hair and weight domains. BES results were not significantly higher in the PCOS group than in the control group (p = 0.727). The main predictors for total HRQoL were PCOS diagnosis per se (\beta = –1.002; p 0.001), BES score (\beta = –0.27; p = 0.004) and body mass index (BMI) percentile (\beta = –0.007; p = 0.013). Conclusions: The lower HRQoL in adolescents with PCOS is attributable to the diagnosis of PCOS, BES score and BMI percentile, confirming the importance of tailoring clinical interventions and counselling to address the domains (i.e., symptoms of hirsutism and weight concerns) causing distress and lowering HRQoL. Further implementation research is required to evaluate the impact of targeted interventions on the HRQoL of adolescent girls with PCOS.