Abstract Background and purpose Reactivation of hepatitis B virus (HBV) happens after systemic chemotherapy, transarterial chemoembolization (TACE) or hepatic resection for HBV-related hepatocellular carcinoma (HCC) patients. The incidence and risk factors of HBV reactivation after radiofrequency ablation (RFA) are unclear. Patients and methods From August 2006 to August 2011, 218 consecutive patients with HBV-related small HCC treated with RFA (n = 125) or hepatic resection (n = 93) were retrospectively studied. The incidence of HBV reactivation and risk factors were analyzed. Results HBV reactivation developed in 20 (9.2%) patients after treatment. The incidence of HBV reactivation was significantly lower in the RFA group (5.6%, 7/125) than the hepatic resection group (14.0%, 13/93, P = 0.034). On univariate and multivariate analyses, no antiviral therapy (OR 11.7; 95% CI 1.52–90.8, P = 0.018) and treatment with RFA/hepatic resection (OR3.36; 95% CI 1.26–8.97, P = 0.016) were significant risk factors of HBV reactivation. On subgroup analysis, the incidence of HBV reactivation was lower in patients who received antiviral therapy than those who did not receive antiviral therapy in both the hepatic resection group (2.9% vs. 20.7%, P = 0.027) and the RFA group (0% vs. 7.6%, P = 0.188), although the difference was not significant in the latter group. Conclusion The incidence of HBV reactivation after RFA was relatively low when compared with hepatic resection. Prophylactic antiviral therapy is recommended, especially for patients who are going to receive hepatic resection for HBV-related HCC to decrease the incidence of post-treatment HBV reactivation.