The increasing power dissipation and decreasing dimensions of microelectronic devices have emphasized the demand for extremely efficient compact cooling technology. Microchannel heat sinks are of particular interest due to high rates of heat transfer, which have become known as one of the effective cooling technologies. In the present work, numerical simulation of incompressible flow in two dimensional microchannels by implementing nonuniform electrokinetic forces is performed using finite volume method. The velocity field and the heat transfer rate are influenced by the wall potential variations through the microchannel. Nondimensional parameters of heat transfer and fluid flows, Debay Huckel length, microchannel size and wall charge potential distribution, have major roles in this investigation. For fixed values of Reynolds number and microchannel size, the patterns of wall potentials are optimized to enhance the heat transfer rate. Velocity profiles are computed and temperature distribution and Nusselt number are obtained for uniform wall heat flux boundary condition. Average and local Nusselt numbers are illustrated for different wall potential configurations and Reynolds number. Velocity vectors and pressure drop are presented for different zeta potentials and Reynolds numbers. Finally, results of nonuniform electrical force are compared to uniform ones.