BackgroundART in women with endometriosis is associated with poor quality of the retrieved oocytes and lower fertilization and pregnancy rates, reflecting that endometriosis may influence fertility by altering the quality of both the oocyte and embryo quality and also by impairing the endometrial receptivity. On comparing endometriosis-affected patients to healthy counterparts, many differences were demonstrated at the endometrial level. Thus, choosing the appropriate method of embryo transfer is of utmost importance, particularly for patients with advanced endometriosis.ObjectiveThe aim of the present study was to compare the reproductive outcomes between fresh and frozen embryo transfer cycles in women with advanced endometriosis.Material and methodsA retrospective cohort study was conducted in the period from January 2018 until December 2021 for patients recruited from two IVF centers, Alexandria, Egypt. Careful review of paper and electronic medical records of infertile women (primary, relative, or secondary infertility) aged 18–37 years who were diagnosed with advanced endometriosis by means of laparoscopy and were scheduled for ICSI followed by either fresh embryo transfer (group I) or freeze-all embryos and deferred embryo transfer (group II) of day 5 embryo(s) was included in the study.ResultsTwo-hundred and eleven women were eligible and included in the study. Women in each study group were matched regarding baseline characteristics. Clinical pregnancy, implantation, and ongoing pregnancy rates were statistically significantly higher in the group of frozen embryo transfer (p < 0.001). Miscarriage rate was found to be higher in the group of fresh transfer compared to FET group but without a statistical significance (20.9% vs 9.2%, p = 0.072).ConclusionIn women with advanced endometriosis, freeze-all policy seems to be associated with better implantation, ongoing pregnancy rates.