Thermal ablation of tumors is a minimally invasive technique more and more employed in cancer treatments. The main shortcomings of this technique are, on the one hand, the risk of an incomplete ablation, and on the other hand, the destruction of the surrounding healthy tissue. In this work, thermal ablation of a spherical hepatocellular carcinoma tumor (HCC) surrounded by healthy tissue is modeled. A modified porous media-based bioheat model is employed, including porosity variability from tumor core to healthy tissue, following experimental in vivo measures. Moreover, three different protocols are investigated: a constant heating protocol, a pulsating protocol, and a new developed damage-controlled protocol. The proposed damage-controlled protocol changes the heating source from constant to pulsating according to the thermal damage probability on the tumor rim. The equations are numerically solved by means of the commercial software COMSOL Multiphysics, and the outcomes show that the new proposed protocol is able to achieve the complete ablation in less time than the completely pulsating protocol, and to reach tissue temperature on the tumor rim 10 °C smaller than the constant protocol. These results are relevant to develop and improve different patient-based and automated protocols which can be embedded in medical devices’ software or in mobile applications, supporting medical staff with innovative technical solutions.