Disclosed are a method and an apparatus for removing condensed water in a gas diffusion layer and a catalyst layer of a fuel cell. The method comprises steps of: a step of determining whether the condensed water is generated in the gas diffusion layer and the catalyst layer of the fuel cell; a step of reducing and supplying an amount of air supplied to a cathode of the fuel cell at a predetermined level, when it is determined that the condensed water is generated in the gas diffusion layer and the catalyst layer in the step of determining; a step of measuring a temperature of a stack of the fuel cell; and a step of increasing the amount of air supplied to the cathode of the fuel cell to an amount of air prior to being reduced at the predetermined operation level, when the measured temperature of the stack of the fuel cell is elevated to a predetermined temperature.