An air compressor control method for a fuel cell vehicle is provided. The method includes sensing variation information of a rotation speed of an air compressor motor and sensing a state of charge (SOC) of a high voltage battery by the fuel cell controller when the rotation speed of the air compressor motor is reduced. An allowable current from regenerative braking of an air compressor is derived using current consumption of an electric or electronic sub-assembly for a fuel cell vehicle in response to determining that the SOC exceeds a predetermined level of the SOC. The air compressor motor is then operated based on the allowable current from regenerative braking by an air compressor controller.