Although numerous studies have attempted to establish the relationship between adenomyosis and infertility, no consensus has emerged. Our aim was to investigate whether adenomyosis and endometriosis affected IVF outcomes in our patients. This was a retrospective study of 1720 patients from January 2016 to December 2019. In total, 1389 cycles were included: 229 cycles in the endometriosis group (group E), 89 cycles in the adenomyosis group (group A), 69 cycles in the endometriosis and adenomyosis group (group EA), and 1002 cycles in the control group (group C). Most patients in groups A and EA received GnRH agonist treatment before FET. The 1st FET live birth rates (LBR) were 39.3%, 32.1%, 25% and 48.1% in groups E, A, EA, and C. The miscarriage rates were 19.9%, 34.7%, 39%, and 17.6%. The per retrieval cycle cumulative live birth rates (cLBRs) in patients < 38 y/o were 56.4%, 58.1%, 44.8%, and 63%. The per retrieval cycle cLBRs in patients ≥ 38 y/o were 25%, 9.8%, 17.2%, and 29.5%. Among groups A and EA, LBRs were 25.58% and 18.89% in patients with a ≥ sevenfold decrease and a < sevenfold decrease in CA-125 level, respectively, after GnRH agonist treatment. Endometriosis was not associated with a poorer pregnancy outcome. Patients with adenomyosis with/without endometriosis had higher miscarriage rates, lower LBRs, and lower cLBRs, especially in patients aged ≥ 38 years, even after GnRH agonist treatment before FET cycles. Patients who have a greater than sevenfold decrease in CA-125 level after GnRH agonist treatment might have better clinical pregnancy outcomes.