Background: Polycystic ovarian syndrome (PCOS) is an endocrinopathy that causes various metabolic syndromes, including insulin resistance in 20-40% of patients. The treatment of the condition is often carried out using metformin, but it has been reported to have different gastrointestinal side effects. Consequently, several studies have recommended the use of propolis as an alternative, which has proven effective in improving insulin resistance in diabetic-induced rats and causes fewer side effects. Objective: This study aimed to compare the effects of propolis and metformin in treating insulin resistance based on homeostasis model assessment of insulin resistance (HOMA-IR) value. Materials and Methods: This study used post-test-only randomized control trial design and the sample population comprised 30 Wistar rats. The animals were divided into 5 groups: control (C), PCOS (PCO), PCOS with metformin (PCO+M), PCOS with propolis extract (PCO+P), and PCOS with metformin and propolis extract (PCO+MP). Subsequently, blood sampling, ovarian tissue sampling, and vaginal smearing were performed after 28 days of treatment. Results: PCO+P and PCO+M groups experienced a significant decrease in testosterone concentration and preantral follicle count compared to PCOS group but the anovulation cycle was similar. Fasting blood glucose concentration in PCO+MP group showed a significant decrease compared to others. However, fasting insulin concentration and HOMA-IR value in treatment groups did not show any reduction compared to PCOS group. Conclusion: Based on the results, propolis extract and metformin could not improve insulin resistance based on HOMA-IR value. However, propolis extract had better hypoglycaemic effects compared to metformin. The combination of both treatments had the potential to lower fasting glucose concentration.