Background: Fractional CO{}_2 laser (FCL) has been gradually used in the management of genitourinary syndrome of menopause (GSM) in recent years, but the results remain uncertain. We aimed to estimate the efficacy and safety of FCL as a novel treatment for controlling the GSM, especially sexual dysfunction, compared with intravaginal estrogen. Methods: The following digital databases were searched, including PubMed, Web of Science, Cochrane Library, and Embase. All the studies were limited to randomized controlled trials (RCTs). Included literatures must be in English, without limitation about region and race. The pooled dates were analyzed by Review Manger version 5.4 (Cochrane Collaboration’s Information Management System, London, UK). Results: 3 RCTs were included, which involved 160 patients, 79 of whom received FCL treatment, 81 received intravaginal estrogen treatments. This meta-analysis results showed no statistical significance existed in improving the patient’s vaginal health index (VHI) (mean difference (MD) = 0.59; 95% confidence interval (95% CI): –1.07~2.25; p = 0.49) after FCL treatment. In terms of the female sexual function index (FSFI) total scores, we observed no improvement without statistical significance (MD = –0.13; 95% CI: –3.32~3.06; p = 0.94). Furthermore, all the FSFI domains showed no statistical significance. No serious complications were reported in all included trials. Conclusions: FCL therapy was an interesting and novel treatment for menopausal female sexual dysfunction. However, no statistical evidence existed, which recommended that FCL was superior to intravaginal estrogen. Our results will be confirmed by high-quality and multicentric RCTs in the future.