Background: Previous studies have reported contradictory results regarding the effectiveness of metformin and myo-inositol on improving reproductive outcomes in patients with polycystic ovary syndrome (PCOS). Therefore, this study aimed to compare the effectiveness of these two drugs on improving reproductive outcomes of PCOS patients undergoing in vitro fertilization (IVF) treatment. Methods: This double-blind randomized clinical trial study was conducted on 140 infertile women with PCOS who were scheduled to undergo IVF in Yas Hospital, Tehran, Iran in 2020. The patients were randomly divided into two groups, including metformin and combination of myo-inositol and folic acid treatment groups. Reproductive outcomes were compared between the two groups. Results: The mean age of the patients was 30.66 ± 5.7 years (30.51 ± 5.88 in metformin treatment group and 30.9 ± 5.53 in myo-inositol group, P = 0.68). There was no significant difference between the two groups regarding the reproductive outcomes, including pregnancy rate, change in BMI, number and quality of oocytes, number and quality of embryos, follicle number, follicle size, ectopic pregnancy rate, and abortion rate (P > 0.05). Conclusion: There is no significant difference in the effect of metformin and myo-inositol on improving reproductive outcomes. Therefore, due to the lack of significant differences in the effectiveness of these two drugs and considering their availability and cost, one of them can be prescribed for the patients.