The hyper androgenic status is a major complication of polycystic ovarian syndrome (PCOS) that deteriorates endometrial function and increases miscarriage rate. This study was conducted to investigate the efficacy of GnRH agonist before frozen-thawed embryo transfer in improving pregnancy outcome in infertile women with PCOS. This single-blind, randomized controlled trial was performed at Dr Shariati hospital and Omid Fertility Clinic in Tehran, Iran. In the study were included 178 PCOS women. Patients were then divided into two groups of control and intervention. All women received the standard treatment for the preparation of the endometrial using estradiol valerate at dose of 6-8 mg/day. The intervention group also received diphereline, as GnRH agonist, at two doses, 8 weeks before starting the endometrial preparation. Chemical pregnancy in intervention group was 47.7% compared to 35.6% in the control group, revealing no significant difference between two groups. No statistically significant difference was observed between two groups concerning clinical pregnancy rate (43.2% vs. 27.3%). However, rate of ongoing pregnancy was 42.0% in intervention group but 18.0% in the control group, suggesting a significant difference (P=0.001). The rate of miscarriage in the intervention group was 2.6% and in the control group was 33.3%, which was significantly lower (P=0.001). It can be concluded that endometrial preparation using GnRH improves ongoing pregnancy and decreases miscarriage rate. It seems that reduction of androgen level in PCOS patients affects the endometrium and improves the receptivity and implantation of the embryo, resulting in better pregnancy outcomes by reducing the miscarriage rate.