Heat transfer in microscale and rarefied gaseous flows has been investigated for high Knudsen number (Kn) flows using the Direct Simulation Monte Carlo (DSMC) method. A wide range of Kn [0.05 – 5], pressure ratio [1.2 – 4] and wall temperature [323 K – 723 K] is studied. The heat flux and local Nusselt number (Nu) are found to exhibit three distinct sections along the length of the microchannel – heat transfer-dominated section, constant heat transfer section and exit section. The defining roles of different effects such as non-equilibrium conditions at the wall, viscous dissipation, axial conduction, pressure work, and shear work have been considered implicitly in the DSMC method. These parameters are seen to influence the heat transfer differently at lower and higher Kn. These results help to quantify the fraction of total heat exchange and reveals the complex interplay of various terms of the energy equation in gas flow in microchannels.