A membrane electrode assembly in a fuel cell system includes a cathode electrode that includes a support layer; a catalyst layer; and a first carbon layer and second carbon layer between the support layer and the catalyst layer, the first carbon layer having a relatively higher porosity and the second carbon layer having a relatively lower porosity. Therefore, the membrane electrode assembly maintains good ion conductivity in the polymer electrolyte membrane by suppressing the movement of water molecules from the polymer electrolyte membrane to the cathode electrode using a water pressure between two carbon layers having different porosity. Also, a flooding phenomenon in the cathode electrode is prevented, thereby maintaining the smooth movement of the oxidizing agent in the cathode.