In one aspect a method for controlling a fuel cell vehicle is provided, comprising generating a torque (TACCEL) calculated based or an accelerator pedal depression value upon completion of start-up of a fuel cell and entering a fuel cell only mode; performing a torque limit control for the torque (TACCEL) calculated based on the accelerator pedal depression value; performing charging from the fuel cell to a power storage means while the vehicle moves slowly by the torque limit control under the fuel cell only mode; and directly connecting the fuel cell to the power storage means by a main relay to enter a hybrid mode, when a voltage difference between the fuel cell and the power storage means is within a predetermined range. Preferred methods can protect the fuel cell, reduce the time for vehicle start-up and improve driving performance.