The present disclosure relates to an apparatus and a method for controlling a steer-by-wire system. In more details, the present disclosure relates to an apparatus and method for determining whether a catch-up is occurred due to a counter electromotive force in a rack drive motor in a steer-by-wire system and reflecting torque information that has not been output due to the catch-up on a steering reaction force motor, and thus providing an accurate steering sense for a driver.