An air shut-off valve apparatus for a fuel cell system and a method of controlling the same are provided. In particular, hydrogen injected into a fuel cell stack is discharged by being diluted with external air when starting the fuel cell system. The apparatus includes a valve body that has an inlet air path connected to a cathode of the fuel cell stack and through which air injected into the fuel cell stack flows, and an outlet air path through which air discharged from the fuel cell stack flows. A bypass body is provided and includes a bypass air path that connects the inlet air path and the outlet air path and a valve flap is disposed at the valve body and opens and closes the inlet and outlet air paths at a first side thereof, and the bypass air path at a second side thereof.