A method and system for controlling a fuel cell vehicle are provided in which a bidirectional converter monitors a state of a fuel cell vehicle in real time to improve control responsiveness in a transient state of the fuel cell vehicle. The method includes receiving, by a bidirectional converter, a command for a current limiting value in the high voltage battery from the fuel cell controller while the fuel cell vehicle is driven. In addition, the bidirectional converter is configured to determine whether the fuel cell vehicle is switched to a predetermined mode and change the current limiting value of the high voltage battery. A predetermined control is performed by the bidirectional converter based on the changed current limiting value when the fuel cell vehicle is switched to the predetermined mode.