In this study, a dental short pulse laser with a Gaussian beam profile was applied normally to the top surface of a mineral organ i.e. the human tooth for a root canal therapy. A numerical method of finite difference is adopted to solve the time-dependent heat transfer equation. The real boundary conditions of thermal insulation on the sharp segment of the root canal and periodic heat flux on the top boundary of the tooth were applied. The comparison of a three-phase-lag (TPL) bio-heat transfer model with other heat transfer studies has shown that this new bio-heat model (TPL) could accurately predict the thermal behaviour of a non-homogeneous structure such as the human tooth. It was observed that decreasing of the pulse time, increasing of the pulse number and laser spot radius are the logical approaches for dental pulp ablation in comparison with increasing of laser intensity or increment of continuous irradiation time. Based on the results of this investigation, an optimum dental laser with heat flux of 5 W/cm2 that could make adequate temperature increments in the range of 5 °C to 8 °C inside the dental pulp after 30 s is suggested. The time of each pulse was 0.1 s, and eight times were iterated in the first ten seconds of treatment time while the laser radius was 3 mm. © 2018