The control objective in hard disk drives is to move head as fast as possible to target track and position the head over the center of target track in the presence of external disturbances. The external shock or disk clamping error in manufacturing process causes the disk center to deviate from the disk rotation center. The disk shift acts on the control system as disturbance and degrades severely the performance of disk drives. In this paper, we present a new controller that compensates for the periodic disturbances very fast. The disturbance compensator is arranged in parallel with the state feedback controller. To avoid the interference with the state feedback controller, the compensator creates compensation signal without the feedback of system output until steady state. The pulse type controller is included additionally for improving the transient performance due to initial state. Finally, in order to demonstrate the superior performance of the proposed compensator. we present some experimental results using a commercially available disk drive.