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Background The effectiveness and safety of focused ultrasound ablation surgery (FUAS) for primary hepatocellular carcinoma (HCC) treatment has not been fully evaluated. This study analyzed the effectiveness and safety of FUAS compared to radiofrequency ablation (RFA). Methods Studies published before November 1, 2020, in the following databases were analyzed: PubMed, Embase, Cochrane Library, Web of Science, Wanfang Data, CqVip, China National Knowledge Infrastructure (CNKI), and Chinese Biomedical (CBM) database. All publications were reviewed independently by two authors. Both randomized controlled trials (RCTs) and cohort studies examining the effectiveness and safety of FUAS and RFA were considered. RCTs and cohort studies’ methodological quality were evaluated using the Cochrane collaboration tool and the Newcastle-Ottawa Scale, respectively. Results A total of 6,597 records were identified, from which 3 cohort studies were selected for quantitative synthesis. All studies had relatively high methodological quality. The meta-analysis indicated that FUAS and RFA had comparable 3-month overall survival (OS) rates [risk ratio (RR): 0.99, 95% confidence interval (CI): 0.86 to 1.14], 6-month OS rates (RR: 1.03, 95% CI: 0.82 to 1.29), and 1-year OS rates (RR: 0.96, 95% CI: 0.84 to 1.11). Also, individual studies reported that the tumor response (reflected by tumor response and tumor ablation rate) and posttreatment complications were comparable between patients treated with FUAS and patients treated with RFA. Due to the limited number of studies reporting tumor response and posttreatment complications, further meta-analyses could not be conducted. Discussion FUAS and RFA were comparable in terms of effectiveness and safety in the treatment of primary HCC. However, current evidence is limited, and more prospective RCTs are warranted to confirm these findings.