This retrospective cohort study evaluates the clinical effects of an antagonist protocol on in vitro fertilization and intracytoplasmic sperm injection among infertile women with polycystic ovary syndrome. A propensity score matching analysis was conducted of 402 infertile women diagnosed with polycystic ovary syndrome undergoing in vitro fertilization/intracytoplasmic sperm injection cycles. The patients were divided into 2 groups: GnRH antagonist (GnRH-ant) pretreatment protocol (n = 202) and non-pretreatment protocol (n = 200). The primary outcome was the high-quality embryo rate. The metaphase II (MII) oocyte rate was calculated. After adjusting for confounders, the high-quality embryo rate (48.29% vs 42.74%, P = .010) was found to be significantly higher in the pretreatment group. However, the number of retrieved oocytes (12.00 vs 12.00, P = .878), the MII oocyte rate (76.6% vs 76.0%, P = .663), the incidence of ovarian hyperstimulation syndrome (6.82% vs 2.27%, P > .05), and the cycle cancelation rate (51.52% vs 51.52%, P > .05) were not significantly different between the 2 groups. Similar results were obtained in the propensity score matching analysis of live birth rate (LBR, 46.88% vs 40.63%, P = .476). GnRH-ant pretreatment protocol resulted in increased high-quality embryo rates without increasing the cycle cancelation rate and the incidence of ovarian hyperstimulation syndrome. The number of retrieved oocytes, the MII oocyte rate, and the clinical pregnancy outcomes did not differ after GnRH-ant pretreatment.