In this paper, 2D electromagnetohydrodynamic (EMHD) flow in a microparallel channel with slightly transverse corrugated walls is investigated using perturbation method. The corrugations of the two walls are presented by periodic sinusoidal waves with small amplitudes. The perturbation solutions of the stream function and a relation between flow rate and roughness are obtained. It is shown that the flow rate always decreases due to the wall corrugations irrespective of the phase difference. For prescribed Hartmann number and wave number of the wavy walls, the flow resistance increases as the phase difference between the wall corrugations increases. The effect of corrugation on the flow rate decreases with Hartmann number. With the increase of wave number, the effects of corrugations on the flow rate increase. The phase difference of wall corrugations becomes unimportant when the wave number is greater than 4. The obtained results for the flow rates as a function of the applied current are in qualitative agreement with the existing experimental results.