A fuel cell system and method of removing impurities from a catalyst are provided. The fuel cell system comprises a fuel cell stack comprising a pair of end plates and at least one unit cell. The unit cell contains a gas diffusion layer in contact with a membrane electrode assembly which is constructed of a polymer electrolyte membrane enclosed between two electrodes. The at least one unit cell is stacked between the end plates. The fuel cell system further comprises a voltage supply means and a means of impressing a cyclically varying voltage from the voltage supply means on the fuel cell stack. The cyclically varying voltage removes impurities that adhere to catalysts on the electrode surfaces in the fuel cell stack.