A dynamic 3D thermoelectric model has been developed to calculate the temperature field and emitter current density in the comb structure of a heterojunction bipolar transistor (HBT) with the length of the emitter metallization paths comparable to the size of the crystal, taking into account the inhomogeneous distribution of current density under the emitter paths caused by a voltage drop on the resistance of the current-carrying metallization. The model is based on an iterative solution in the COMSOL Multiphysics software environment of a non-stationary heat equation together with a system of equations for the distribution of electric potential along the emitter path and the current density under the path. It is shown that during the action of the heating power pulse in the HBT, the distribution of temperature and current density along the emitter tracks change character, respectively, from homogeneous and monotonically decreasing to non-monotonically changing. At the same time, the maximum temperature and current density reach stationary values with a rate significantly exceeding the rate of overheating increase with homogeneous heating of the structure, and the maxima of temperature and current density in the process of self-heating shift from the beginning to the center of the tracks. The proposed model can be used to evaluate the thermomechanical stresses in the structure of the HBT and the limiting electrical parameters in the pulsed modes of operation of the HBT.