SUMMARYA meshless numerical method is proposed for the solution of the transient bioheat equation in two and three dimensions. The Pennes bioheat equation is extended in order to incorporate water evaporation, tissue damage, and temperature‐dependent tissue properties during tumor ablation. The conductivity of the tissue is not assumed constant but is treated as a local function to simulate local variability due to the existence of usually unclear interfacing of healthy and pathological segments. In this way, one avoids the need for accurate identification of the boundaries between pathological and healthy regions, which is a typical problem in medical practice, and sidesteps, evidently, the corresponding mathematical treatment of such boundaries, which is usually a tedious procedure with some inevitable degree of approximation. The numerical results of the new method for test applications of the bioheat transfer equation are validated against analytical predictions and predictions of other numerical methods. 3D simulations are presented that involve the modeling of tumor ablation and account for metabolic heat generation, blood perfusion, and heat ablation using realistic values for the various parameters. An evaluation of the effective medium approximation to homogenize conductivity fields for use with the bioheat equation is also provided. Copyright © 2014 John Wiley & Sons, Ltd.