A system and a method are provided for controlling emergency driving of a fuel cell vehicle. The system includes a cutoff relay that connects or cuts off a current flow between a chopper and a supercapacitor. A connecting relay connects or cuts off a current flow between a power line to which a fuel cell and a driving motor are connected and the supercapacitor. An emergency driving relay includes a first terminal connected to a line branched from a ground line to which the fuel cell and the driving motor are connected and a second terminal connected between a braking resistor and the chopper. A power system controller is driven in an emergency driving mode to cutoff relay to be turned off and the connecting relay to be turned on during a short circuit of the chopper and turns the emergency driving relay on or off.