In present paper, we simulate the electro-kinetic transport of aqueous solution through a microchannel containing porous media. The micro-channel walls are simulated as complex wavy surface and are modelled by superimposing the three wave functions of different amplitudes but the same wavelength. The micro-channel contains an isotropic, homogenous porous medium, which is analysed with a generalized Darcy law. The nonlinear-coupled governing equations for mass, momentum and electrical potential conservation are simplified using low Reynolds number and long wavelength approximations, and the Debye electro-kinetic linearization. Following non-dimensional transformation of the linearized boundary value problem, closed-form analytical solutions are presented for the velocity components, pressure gradient, local wall shear stress, average flow rate and stream function subject to physically appropriate boundary conditions. Validation with a finite difference method is also conducted. The effect of permeability parameter, Debye length (i.e. characteristic thickness of electrical double layer) and electro-osmotic velocity on flow characteristics is illustrated graphically and interpreted at length. The study finds applications in chromatography, hybrid electro-osmotic micro-pumps, transport phenomena in chemical engineering and energy systems exploiting electro-kinetics.