A fuel cell system and a method for controlling the same are provided. The method includes rapidly increasing an angular speed of a rotating magnetic field of an induction motor to maximize iron loss of the induction motor, thereby resulting in an increase in the temperature of a rise cell stack. The method further includes eliminating torque of a driving motor generated by an increase in the angular speed of the rotating magnetic field, using a torque eliminator. The torque eliminator includes a P-stage reducer or a hydraulic break.