A control system which is capable of compensating for and suppressing the influence of a periodic disturbance on a controlled object more quickly, even when the controlled object is subjected to the periodic disturbance the amplitude of which periodically changes, thereby enhancing the stability and the accuracy of control. The control system includes an ECU. The ECU calculates disturbance compensation values for compensating for a periodic disturbance by searching maps and tables, in timing of generation of each pulse of a CRK signal. The ECU calculates control inputs at a predetermined control period, with predetermined control algorithms, according to the disturbance compensation values read in at the control period, respectively.