An apparatus and a method for discharging a residual electric energy of a fuel cell can rapidly discharge and remove a residual electric energy of a fuel cell for safety after the fuel cell is operated or when a collision is detected. The apparatus for discharging the residual electric energy of the fuel cell includes: a discharge relay connected with a fuel cell and turned on when starting or stopping a vehicle or a collision detecting sensor detects a collision; and a non-linear protecting element connected with the discharge relay in order to discharge a residual electric energy from the fuel cell.