The present invention relates to a method and a system for compensating for a position error of a step motor. A method for compensating for a position error of a step motor includes: sequentially inputting a predetermined number of a pulse as a rotator position command to a step motor driver; driving a step motor in a micro step method based on the rotator position command and a predetermined current command table; detecting an actual position of a rotator of the step motor while the step motor is being driven; calculating a position error by comparing the rotator position command and the detected actual position of the rotator; and compensating for the predetermined current command table based on the calculated position error. According to the present invention, a position error which may occur when the step motor is driven by a micro step method can be removed.