An apparatus is provided for driving wheels for an in-wheel system, including: a driving shaft which is the center of rotatable driving; a fixation supporter rotatably supporting the driving shaft and coupled to the driving shaft; an in-wheel motor generating rotational power, which is coupled to the inside of a wheel in which a tire is mounted on one driving shaft in a shaft direction of the fixation supporter; and a balancing member formed on the other driving shaft in the shaft direction of the fixation supporter and formed at a position corresponding to the wheel coupled with the in-wheel motor. According to the present invention, an eccentricity phenomenon which is caused due to inclination of a wheel and a motor in one direction of a fixation supporter can he prevented in an apparatus of driving wheels for an in-wheel system.