A restarting system, a controller, and a restarting method for a fuel cell vehicle are provided. The restarting system includes a consumption resistor connected in parallel to a high voltage line that connects between a fuel cell and a high voltage battery and a relay that adjusts the connection between the consumption resistor and the high voltage line. A controller operates the relay and when a shutdown request signal of the vehicle is input, charges the high voltage battery with residual generated power of the fuel cell or connects the relay to the consumption resistor to consume the residual generated power as the consumption resistance. When a starting request signal of the vehicle is input, the controller is reset when an output voltage of the fuel cell is reduced to be equal to or less than a required voltage and then output a starting permission signal of the vehicle.