Objectives To compare the efficacies of catheter-directed sclerotherapy (CDS) with 99% ethanol and surgery for ovarian endometrioma and their impact on the ovarian reserve. Methods From January 2011 to June 2019, 71 patients who underwent surgical excision (n = 51) or CDS (n = 20) for symptomatic ovarian endometriomas were reviewed. To analyze the effect on the ovarian reserve, serum anti-Mullerian hormone (AMH) levels were compared before and after the procedure. Symptoms, serum cancer antigen 125 (CA-125), lesion size, recurrence, hospitalization, and complications were reviewed retrospectively. Results During a mean follow-up of 22.3 months (range, 6 to 94 months), no significant difference in symptom relief was found between CDS and surgery (95.0% [19/20] and 92.2% [47/51], respectively,p > 0.999). The hospital stay was shorter with CDS than with surgery (2.6 +/- 0.6 days and 4.1 +/- 0.5 days, respectively,p < 0.001). There was no significant difference in serum AMH levels before and after CDS (2.3 (interquartile range (IQR) 1.1-5.3) ng/mL and 2.6 (IQR 0.9-4.9) ng/mL, respectively,p = 0.243), but there was a significant decrease in serum AMH in the surgery group (3.0 (IQR 1.3-5.5) ng/mL and 1.6 (IQR 0.7-3.2) ng/mL, respectively,p < 0.001). CA-125 decreased in both CDS and surgery groups (p = 0.001 and < 0.001, respectively). Two minor complications occurred in the surgery group, while no complication was observed in the CDS group. Conclusions The therapeutic efficacy of CDS appears to be comparable to that of surgical resection for ovarian endometrioma. Ovarian function was well-preserved, and a shorter hospital stay was required in patients who underwent CDS.