Fractured porous media is of great significance to the exploration and development of unconventional reservoirs. In this paper, a fractal model for permeability through micro-fractured porous media with consideration of the electric double layer (EDL) effect is proposed based on the fractal theory. The present model indicates that the permeability is a function of the electrokinetic parameters and micro-structural parameters of fractured porous media, and each parameter has a clear physical meaning, the results from the proposed model are found to be in good agreement with experimental data. Moreover, factors influencing the permeability are also analyzed in detail. The results indicate that the more obvious EDL effects will lead to permeability becoming lower. The present fractal model for the permeability with the EDL effect can provide guidance for tight reservoir development or other micro-porous media transportation.