The invention provides a method for preparing a membrane electrode of a fuel cell, comprising the steps of preparing diffusion layers, and superimposing the diffusion layers on a proton exchange membrane having a catalyst layer on each surface, wherein the method for preparing the proton exchange membrane having a catalyst layer on each surface comprises the steps of: filling a catalyst slurry containing a catalyst and a bonding agent between two polymer films, and pressing the polymer films filled with the catalyst slurry to obtain a catalyst layer; and superimposing the catalyst layer on each surface of a proton exchange membrane. The method of the present invention can control the thickness of the catalyst layers by pressing during preparation thereof, therefore, the catalyst layers have an even thickness and surface.