A method for controlling an operation of a fuel cell of a fuel cell vehicle is provided. The method includes detecting a state of charge (SOC) of a high voltage battery and determining whether the detected SOC of the high voltage battery is within or beyond a preset range from a minimum recommended SOC to a maximum recommended SOC. Power generation of the fuel cell is performed or stopped by comparing a required current of the vehicle with a preset current value required to enter a fuel-cell stop mode in which the power generation of the fuel cell is stopped and a preset current value required to release the fuel-cell stop mode.