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The purpose of this study was to systematically evaluate the prognosis of patients with hepatocellular carcinoma (HCC) smaller than 5 cm using microwave ablation (MWA) versus radiofrequency ablation (RFA). PubMed, Cochrane Library and Embase databases were searched for studies reporting comparisons of two interventions (MWA versus RFA) for patients with early-stage HCC published up to 31 December, 2022. The analysis evaluated the recurrence-free survival (RFS), overall survival (OS) and complications. A total of 894 patients were enrolled in six studies (two randomised controlled trials and four propensity score cohort studies). There were 446 patients in the MWA group and 448 patients in the RFA group. Compared with RFA, MWA had a significant advantage in the post-operative 1-, 2-, 3- and 5-year RFS (odds ratios [OR] = 0.58, 95% confidence interval [CI]: 0.40, 0.84; OR = 0.60, 95% CI: 0.45, 0.80; OR = 0.56, 95% CI: 0.33, 0.93; and OR = 0.44, 95% CI: 0.30, 0.65). The OS of MWA was significantly higher than that of RFA in 5 years after ablation (OR = 0.48, 95% CI: 0.34, 0.68). Moreover, MWA had an advantage in the incidence of complications (OR = 2.23, 95% CI: 1.16, 4.29). In the comparison of percutaneous MWA and RFA in the treatment of HCC with a diameter smaller than 5 cm, MWA may have more advantages in improving the prognosis.