Background: Two protocols are generally performed after the following hysteroscopic resection of septate uterus to prevent Asherman’s syndrome in Iran. The aim of this study was to assess and compare the postoperative complication rate by alternate and constant therapy following hysteroscopic septum resection procedure. Materials and Methods: The authors conducted a retrospective interventional study on secondary data obtained from the medical records of 106 infertile women with septate uterus who underwent a hysteroscopic resection between April 2005 and February 2014. After septum resection, 71 patients received alternate hormonal therapy and 35 patients received constant hormonal therapy. All the women were followed-up postoperatively with interview and physical examination for more than six months. Results: Of the 71 women who received alternate hormonal therapy, 16 (22.5%) had spotting. While in the constant protocol therapy group, the rate of the spotting during the follow-up period was reported in 13 (37.1%) patients. There was no significant difference between the two groups in terms of spotting complication after the septum resection. Self-reported breast tenderness as complications of hormonal therapy after septum resection in constant protocol was greater than in alternate protocol group (21.1% vs. 60.0%) (p < 0.0001). Conclusion: The result of this study indicated that hormonal therapy complications following hysteroscopic resection of septate uterus in both protocols was the same.