According to a manufacturing method for a fuel cell, an insulating member having a plurality of communication holes therein is disposed on a side of a gas diffusion layer, which is formed by stacking a layer made of a carbon fiber and a water-repellent layer, where the water-repellent layer is provided, the gas diffusion layer and the insulating member are sandwiched by a pair of electrodes, and a pair of contact pressure plates are disposed on respective rear surfaces of the pair of electrodes so as to sandwich the pair of electrodes so that the gas diffusion layer is pressurized by the pair of contact pressure plates. When a voltage is applied to the pair of electrodes while maintaining the pressurized state, an electric current flows through a protrusion portion of a carbon fiber which comes in contact with the electrode on the water-repellent layer side via the communication holes of the insulating member, so that the protrusion portion of the carbon fiber is burned and removed by Joule heat. When it is detected that no electric current flows between the electrodes, application of a voltage to the pair of electrodes is stopped, and the pressure in the pressurized state is decreased to a normal pressure state.