Endobiliary radiofrequency ablation (RFA) is a promising treatment option for malignant biliary obstruction, but conventional catheter RFA (Conventional-RFA) has several limitations. We examined the feasibility of a novel approach to balloon-based RFA (Balloon-RFA) with an automatic temperature control system in freshly resected pig livers. Balloon-RFA application was performed in a step-by-step manner at target temperatures of 50°C, 60°C, and 70°C. The temperatures were maintained for 60 s. As a control, Conventional-RFA was performed at 7 W of power for 90 s, 7 W 120 s, 10 W 90 s, and 10 W 120 s. The ablation areas were measured and compared between Balloon-RFA and Conventional-RFA. The maximum ablation depths in Balloon-RFA were 1.86 ± 0.53, 2.29 ± 0.31, and 3.19 ± 0.47 mm at target temperatures of 50, 60, and 70°C, respectively. The maximum ablation depths in Conventional-RFA were 2.81 ± 0.46, 4.09 ± 0.45, 3.41 ± 0.58, and 4.27 ± 0.29 mm at 7 W 90 s, 7 W 120 s, 10 W 90 s, and 10 W 120 s, respectively. Differences between the minimum and maximum depths were significantly smaller in Balloon-RFA (0.73 ± 0.31 mm) than in Conventional-RFA (2.00 ± 0.62 mm; P < 0.001). Excessive ablation occurred only in Conventional-RFA (0% vs. 67%; P = 0.005). The novel balloon-based RFA system allows ablation to be finely tuned in order to successfully obtain consistent ablation depths and avoid excessive ablation.