Polycystic ovary syndrome (PCOS) is one of the most critical disorders, which affects approximately 20% of women of childbearing age and melatonin supplementation in these women can be effective. However, human studies in this area are particularly limited to IVF candidates. The aim of this clinical trial study was to evaluate the effect of melatonin on the in vitro fertilization (IVF) in PCOS involved women. In this clinical trial study, a total of 320 women with PCOS were randomly assigned to the intervention and control groups. Patients in the intervention group (n=160) received a combination of melatonin and metformin (3 mg and 500 mg, respectively) three times a day. The control group (n=160) received metformin 500 mg from the luteal phase of the cycle before the start of gonadotropin. Oocyte and embryo quality, number of oocytes, and pregnancy outcomes were compared in both groups. Our study revealed that the frequency of Metaphase II oocytes (69.9% vs. 57.9%, p＜0.001) and the number of embryos of the top-quality (grade A) were higher in the group treated with melatonin (40.3% vs. 29.9%, p=0.001). The rate of clinical pregnancy and implantation were also higher in the intervention group. The odds of clinical pregnancy in the intervention group was 1.8 times (p=0.039). Moreover, oral melatonin supplementation was effective in patients with PCOS, who were candidates for IVF because of the increased quality of mature oocytes, top-quality embryos, and increased odds of clinical pregnancy.