Two phase pressure drop in microchannels for non-uniform heat flux condition is analyzed in this paper. Homogeneous flow model has been assumed with constant heat flux boundary condition with fixed inlet temperature and outlet pressure. Water and ethanol are taken as working fluids. Modeling scheme is used to do the parametric investigations for total pressure drop. The model has been compared with the experimental results from literature. The results show that the working fluid properties and heat flux distribution play a significant role for overall pressure drop.