There is provided with a positioning control system including: a head moving unit; a position detecting unit detecting a head position at predetermined time intervals; an error detecting unit detecting a position error of the head for a target position; a disturbance detecting unit detecting a non-periodic disturbance; a modifying unit modifying a first position error signal corresponding to a first head position detected in a first rotation period based on a second position error signal corresponding to a second head position detected one period length before; and a feedback controller, wherein the modifying unit modifies the first signal after reducing an amplitude of the second position error signal when a detected timing of the second head position is included in a predetermined time range with respect to a detected timing of the non-periodic disturbance detected in a second rotation period which is one period before the first rotation period.