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Purpose: To investigate the feasibility of three-dimensional contrast-enhanced ultrasound (3DCEUS) fusion in evaluating ablative margin (AM) after radiofrequency ablation (RFA) for hepatocellular carcinoma (HCC) and compare with those of computed tomography (CT) fusion. Patients and methods: In total, 55 patients (47 men, 8 women; mean age, 56.0 ± 10.6 years) with 55 HCCs were included. Pre- and post-RFA 3DCEUS images were fused to assess AM immediately after RFA. The AM measured on fusion imaging was categorized into two groups: (A) AM <5 mm, and (B) AM ≥5 mm. The agreement of AM evaluation was compared between 3DCEUS and CT fusion. The influence of AMs evaluated by 3DCEUS fusion on the risk of local tumor progression (LTP) was assessed. Results: For 3DCEUS fusion, registration success rate was 96.4% (53/55). AM evaluation resulted in 28 tumors in group A and 25 tumors in group B. For CT fusion, AM evaluation resulted in 31 tumors with AM <5 mm and 23 tumors with AM ≥5 mm. AM was successful evaluated by both technique in 53 (96.4%) tumors. The agreement between 3DCEUS and CT fusion was excellent (kappa coefficient = 0.924, p < .001). LTP was identified in 5 tumors (9.4%, 5/53). LTPs all occurred in the area where unachieved 5 mm AM was evaluated by 3DCEUS fusion. Cumulative rate of LTP was significantly higher in group A than in group B (28% versus 0%; p = .033, log-rank test). Conclusions: 3DCEUS fusion enables AM evaluation for HCC immediately after RFA with comparable accuracy to CT fusion. AM <5 mm evaluated by 3DCEUS fusion has high predictive value for LTP.