Studies investigating the alterations of serum irisin and its change with metformin therapy in patients with polycystic ovary syndrome (PCOS) are conflicting. Our aim is to study serum irisin in PCOS patients and the change of irisin levels with metformin therapy over 6 months. This is a randomized control study conducted in 187 PCOS cases and 94 age-matched controls aged 18-40 years. Detailed evaluation of anthropometric, biochemical, and hormonal parameters was performed. A subset of 99 overweight/obese patients with body mass index (BMI) ≥23 kg/m2 were stratified into a metformin group (n = 67) receiving 500 mg thrice daily and a lifestyle intervention-only group (n = 32). The effect of metformin therapy on serum irisin levels was measured at the end of 6 months. Statistical analyses were performed with SPSS version 26.0 Software. Serum irisin was higher in PCOS patients than in controls [12.47 (8.1-17.7) vs 8.3 (7.0-9.6) ng/ml, P < 0.001], independent of BMI. Serum irisin showed a significant positive association with BMI (β =0.168), waist-to-hip ratio (β =0.166), leutinizing hormone (β =0.225), TG (β =0.305), FAI (β =0.151), and testosterone (β =0.135). Serum irisin showed a significant positive association with homeostatic model assessment of insulin resistance (HOMA-IR) (β =0.14, P = 0.04) in overweight/obese PCOS patients only (n = 146) but not in the whole PCOS cohort (n = 187). Metformin reduced the median serum irisin levels significantly (13.9 to 12.1 ng/ml, P < 0.001), and the delta change in irisin levels was associated with HOMA-IR in the metformin group. Serum irisin is increased in PCOS patients independent of BMI. Metformin therapy reduced serum irisin levels in overweight/obese PCOS patients by improving insulin resistance.