An apparatus for compensating a torque of a motor-driven power steering system includes a column torque sensor detecting a column torque applied to a steering shaft; a vehicle speed sensor detecting a vehicle speed; a steering angle sensor detecting a steering angle velocity of a steering wheel; and a control unit suitable for calculating a high frequency assist gain for controlling a high frequency region of the column torque by receiving the column torque and the vehicle speed, determining whether a steering state is a steering reversal state, based on the steering angle velocity received from the steering angle sensor and motor current applied from an MDPS motor, compensating the high frequency assist gain depending on a result of determination, and compensating a high frequency characteristic of an assist torque calculated from the column torque and the vehicle speed, by using the compensated high frequency assist gain.