A three-dimensional numerical model is applied in this study to illustrate the electrical response of a thermoelectric generator (TEG) during transient heat flux at the hot side. In this work, various types of thermal boundary conditions are considered to evaluate the performance of the TEG. Thus, a TEG under pulsed heat flux is studied numerically, and the numerical model is verified by experimental results. With the consideration of a defined reference geometry, different heat flux frequencies are applied in order to evaluate the corresponding electrical output by the TEG. In addition, variation of the module performance for various TEG leg lengths and its cross-sectional area are studied over a wide range of heat fluxes. The results indicate that the open circuit voltage in the experiment is in a good agreement with the open circuit voltage in the simulation results. The results show that the range of power oscillation reduces at higher frequency of the applied heat flux. Furthermore, the variability of the output power increases as the thermoelectric element length increases and the area of the element reduces. Published by AIP Publishing.