Purpose <p>Polycystic ovary syndrome (PCOS) is a common endocrine disorder associated with adverse reproductive and obstetric outcomes, particularly in pregnancies achieved through assisted reproductive technologies. This study aimed to compare obstetric outcomes among programmed cycle-frozen embryo transfer (PC-FET), modified natural cycle-frozen embryo transfer (mNC-FET), and natural cycle-frozen embryo transfer (NC-FET) in women with PCOS using a nationwide Korean health claims database.</p> Methods <p>This population-based cohort study utilized data from the National Health Insurance Service–National Health Information Database of South Korea. A retrospective analysis was conducted on 3,873 PCOS patients with singleton pregnancies following FET between October 2017 and December 2021. Patients were categorized into PC-FET, mNC-FET, and NC-FET groups based on prescription records. Obstetric outcomes were analyzed using logistic regression models adjusted for age and medical comorbidities.</p> Results <p>mN-FET was associated with significantly lower rates of miscarriage (23.9%) compared to PC-FET (31.3%) and NC-FET (32.0%), as well as a higher term birth rate (69.6% vs. 61.7% and 60.2%, respectively). mNC-FET also showed significantly lower rates of hypertensive disorders of pregnancy, gestational hypertension, cesarean section, and emergency cesarean section compared to PC-FET. No significant differences were observed between mNC-FET and NC-FET in most obstetric complications.</p> Conclusion <p>mNC-FET was associated with favorable obstetric outcomes compared to PC-FET and NC-FET in women with PCOS. These findings suggest that mNC-FET may be an effective and safer endometrial preparation strategy in this population. Further prospective studies are needed to validate these results and optimize FET protocols based on individual patient characteristics.</p>