The electromagnetic energy carried by microwaves interacts with human head and produces thermal changes within the head. Conventionally, Pennes’ bioheat transfer equation (BTE) is employed to investigate the thermal changes in biological tissues. Pennes’ equation assumes infinite speed of propagation of heat transfer, however, heterogeneous structures such as biological tissues exhibit relaxation times, which is the time required for accumulation of enough energy to transfer it to the nearest element. In present study, we utilized thermal wave model of bioheat transfer (TWMBT) which incorporates relaxation times to numerically predict temperature changes in six layers human head. Finite element based numerical simulation package COMSOL Multiphysics is employed for the thermal analysis. Numerical scheme comprises coupling of solution of Maxwell's equation of wave propagation within tissue to TWMBT. Temperatures estimated with various values of relaxation time are compared with that by Pennes’ equation. The results show that the transient temperature within human head estimated with relaxation time 10 s, 20 s, and 30 s can be up to 36%, 54%, and 66% lower than predicted by Pennes’ BTE respectively. At longer microwave exposure the influence of relaxation times becomes insignificant and the steady state temperatures predicted by TWMBT and Pennes’ BTE are identical. The findings suggest that inclusion of relaxation times in thermal analysis is of significant importance if the exposure duration is short. The effect of parameters such as microwave power and user age on the temperatures projected with different relaxation times is also investigated.