The present study has numerically investigated two-dimensional electroosmotic flows in a microchannel with dielectric walls of rectangle-waved surface roughness to understand the roughness effect. For the study, numerical simulations are performed by employing the Nernst–Planck equation for the ionic species and the Poisson equation for the electric potential, together with the traditional Navier–Stokes equation. Results show that the steady electroosmotic flow and ionic-species transport in a microscale channel are well predicted by the Poisson–Nernst–Planck model and depend significantly on the shape of surface roughness such as the amplitude and periodic length of wall wave. It is found that the fluid flows along the surface of waved wall without involving any flow separation because of the very strong normal component of EDL (electric double layer) electric field. The flow rate decreases exponentially with the amplitude of wall wave, whereas it increases linearly with the periodic length. It is mainly due to the fact that the external electric-potential distribution plays a crucial role in driving the electroosmotic flow through a microscale channel with surface roughness. Finally, the present results using the Poisson–Nernst–Planck model are compared with those using the traditional Poisson–Boltzmann model which may be valid in these scales.