Background <p>The management of endometriomata remains a challenge, with current options associated with either high recurrence rates or significant reduction in ovarian reserve. Ethanol sclerotherapy has been suggested as a treatment that is effective while maintaining ovarian reserve.</p> Methods <p>PubMed, EMBASE, MEDLINE, SCOPUS and CENTRAL were searched with no restriction on date or language. Keywords and MESH terms for ‘endometrioma’ AND ‘ethanol sclerotherapy’ AND ‘cystectomy’ were used. Studies were included if they made a direct comparison between ethanol sclerotherapy and cystectomy in the management of endometriomata in women of reproductive age. Randomised controlled trials (RCTs), cohort or case control studies were included. Searches were performed 11th February 2025 and repeated 21st August 2025. Risk of bias was assessed using ROB2 for RCTs and ROBINS-I for observational studies.</p> Results <p>Searches identified 172 studies with 16 of these fitting the inclusion criteria.</p> <p>Unfortunately, a formal analysis of between group change in Anti-Mullerian hormone (AMH) was not possible due to insufficient reporting of change score variance data, as such an exploratory between group pre- and post- analysis was performed instead. This found no significant difference in AMH at baseline (mean difference (MD) 0.02, 95% CI –0.20 to 0.25, <i>p</i> = 0.830) while post procedure AMH was significantly higher in the sclerotherapy arm (MD 0.75, 95% CI 0.43 to 1.06, <i>p</i> &lt; 0.001). Overall risk of bias was high; however, similar results were seen following a sensitivity analysis excluding studies at highest risk of bias (high for ROB2 and critical for ROBINS-I) (MD -0.25, 95% CI -0.57 to 0.08, <i>p</i> = 0.136 and MD 0.60, 95% CI 0.22 to 0.97, <i>p</i> = 0.002, respectively). Studies reporting on Antral Follicle Count (AFC) gave conflicting results and all were assessed as at high or critical risk of bias. No significant difference was seen in recurrence (LogOR 0.28, 95% CI –0.57 to 1.12, <i>p</i> = 0.523). Rates of serious complications were low at 0.24% for sclerotherapy and 0.76% for cystectomy. It was not possible to pool data on symptomatology. Number of oocytes retrieved was higher in the sclerotherapy arm (MD 3.23, 95% CI 1.34 to 5.12, <i>p</i> &lt; 0.001). Number of mature oocytes retrieved was also higher in the sclerotherapy arm (MD 2.79, 95% CI 1.08 to 4.51, <i>p</i> = 0.001), however this became non-significant when studies at the highest risk of bias were excluded (MD 0.79, 95% CI -0.61–2.19,<i> p</i> = 0.27). Data on pregnancy rate could not be pooled due to the wide variation in definition of clinical pregnancy. No significant difference was seen in live birth rate between interventions (logOR 0.59, 95% CI -0.30 to 1.48, <i>p</i> = 0.192).</p> Conclusions <p>Our results show ethanol sclerotherapy maintains ovarian reserve when compared to ovarian cystectomy in the treatment of endometrioma, as evidenced by the higher post-procedure AMH levels and increased number of retrieved oocytes at IVF seen following sclerotherapy. However, due to the high risk of bias and flaws in design of included studies, high-quality randomised controlled trials with unified outcome standards are urgently required to confirm these findings and verify the protective benefit of ethanol sclerotherapy. This would support patients and their clinicians in decisions regarding management of endometriomata, particularly when fertility preservation is required.</p> Trial registration <p>This review was prospectively registered with the International Prospective Register of Systematic Reviews (PROSPERO). The registration number is CRD42024625920.</p>