Purpose: The aim of this study was to investigate the effect of human chorionic gonadotropin (hCG) in hormone replacement (HT) regime for frozen thawed embryo transfer in women with endometriosis (EM).Methods: We performed a retrospective, database-search, cohort study and included data on EM patients who underwent frozen embryo transfer (FET) between January 1, 2009 and August 31, 2018. According to the protocols for FET cycle, the patients were divided into two groups: control group (n = 296) and hCG group (n = 355). Clinical pregnancy rate, live birth rate, early abortion rate, late abortion rate, and ectopic pregnancy rate were compared between the two groups.Results: There was a significant increase in clinical pregnancy rate in the hCG group (57.7 vs. 49%, p = 0.027) compared with the control group. The live birth rate in the hCG group (45.6 vs. 38.5%, p = 0.080) was also elevated, but this difference was not statistically significant.Conclusion: hCG administration in HT regime for FET increases the pregnancy rate in women with EM.