A system for compensating for disturbance of a motor for motor driven power steering is provided. The system for compensating for disturbance of a motor for motor driven power steering compensates for the disturbance based on a closed loop based input value prediction model unit, separately predicts an input value from a command by a closed loop based input value prediction model unit, and compensates for disturbance in accordance with a desired disturbance frequency band when there is a difference between the predicted input value and an input value error-compensated by a feedback controller.