A two-dimensional electrothermal model of the bipolar transistor (BJT) is established, and the transient behaviors of the BJT originally in the forward-active region are simulated with the injection of electromagnetic pulse from the base. The results show that the damage location of the BJT shifts with the amplitude of the pulse. With a low pulse amplitude, the burnout of the BJT is caused by the avalanche breakdown of the emitter-base junction, and the damage location lies in the cylindrical region of this junction. With a high pulse amplitude, the damage first occurs at the edge of the base closer to the emitter due to the second breakdown of the p-n-n+ structure composed of the base, the epitaxial layer and the substrate. The burnout time increases with pulse amplitude increasing, while the damage energy changes in a decrease-increase-decrease order with it, thus generating both a minimum value and a maximum value of the damage energy. A comparison between simulation results and experimental ones shows that the transistor model presented in the paper can not only predict the damage location in the BJT under intense electromagnetic pulses, but also obtain the damage energy.