Endometriosis, a common condition in women of reproductive age, has been proven to impair fertility. Prolonged and ultra-long agonist protocols have been shown effective in improving clinical outcomes of IVF/ICSI. The aim of this study was to examine the effectiveness of a modified super-long downregulation protocol (MSDP) on clinical outcomes of IVF/ICSI in patients with endometriosis. Clinical records of a cohort undergoing MSDP and a conventional super-long downregulation protocol (SDP), from October 1, 2013 to February 28, 2016, were retrospectively reviewed. A total of 718 IVF/ICSI cycles were enrolled. IVF/ICSI outcomes were compared between groups. MSDP yielded a significantly higher clinical pregnancy rate (48.6% versus 39%, P<0.05), implantation rate (36.1% vs. 27.3%, P<0.01), and live birth rate per transfer (41.2% vs. 30.9%, P<0.05) than SDP. In endometriosis patients, MSDP also achieved a higher clinical pregnancy rate (56.7% vs. 39.8%, P<0.05), implantation rate (38.7% vs. 28%, P<0.05), and live birth rate per transfer (46.7% vs. 31%, P<0.05). Dosage of gonadotropin administered, duration of gonadotropin administration, fertilization rates, number of high quality embryos, miscarriage rates, and ectopic pregnancy rates were comparable between endometriosis patients with MSDP and SDP. Results of the present study demonstrate that the MSDP protocol yields better IVF/ICSI outcomes for infertile patients with endometriosis. For infertile women with endometriosis, lacking financial support, the MSDP protocol may provide another treatment option.