A disk drive is disclosed comprising a voice coil motor (VCM) for rotating an actuator arm about a pivot in order to actuate a head over a disk. The disk is rotated by a spindle motor, and a feed-forward compensation value is computed that compensate for a non-centric alignment of the disk with respect to the spindle motor. During a calibration mode, the VCM is controlled to press the actuator arm against a crash stop, and the feed-forward compensation value is computed in response to a position error signal (PES). The PES is generated in response to embedded servo sectors recorded on the disk, wherein each embedded servo sector comprises a track address for coarse alignment and servo bursts for fine alignment.