Background Pain-relieving effects of dienogest against endometriosis are comparable to leuprolide acetate for 24 weeks. We assessed whether long-term dienogest administration reduces recurrence after endometrioma excision. Methods In this retrospective cohort study, 568 women with MRI-based diagnosis of ovarian endometrioma, who underwent laparoscopic stripping between 2008 and 2013, were studied. Recurrence rates and side effects over 5 years were investigated in 417 without postoperative medication and 151 who received dienogest postoperatively at 2 mg. Transvaginal sonography was performed every 3 months, and when cystic lesions ≥2 cm were observed, diagnostic MRI was conducted. Recurrence was defined as a lesion previously diagnosed as endometrioma by MRI, equal in size or larger 3 months later on ultrasonography. Cumulative recurrence rates were calculated with the Kaplan-Meier method, and group comparison involved log-rank tests. Blood examinations were completed every 3 months, and bone mineral density was measured with DEXA every 6 months. Results Cumulative recurrence rates at the 5th postoperative year in the no-postoperative-medication and 2-mg dienogest groups were 69 and 4%, respectively, showing significant decreases (odd ratio [OR] = 0.09, 95% confidence interval, 0.03-0.26). Anemia occurred in 4% due to metrorrhagia directly after administration, metrorrhagia including spotting was observed in 20% at 1 year and decreases in bone mineral density and depression were observed in 4 and 2.6%, respectively, in the dienogest group. Conclusions Dienogest significantly prevented postoperative endometrioma recurrence. However, side effects such as metrorrhagia and a decreased bone mineral density were observed. Therefore, careful long-term follow-up is necessary.