A disk drive is disclosed comprising a disk having a plurality of tracks, an actuator arm, a head connected to a distal end of the actuator arm, and a voice coil motor (VCM) for rotating the actuator arm about a pivot to actuate the head over the disk. A driving current is applied to the VCM to control the motion of the actuator arm. A back EMF voltage generated by the VCM is detected, and a velocity of the VCM is estimated in response to the back EMF voltage. The estimated VCM velocity is compared to a target velocity in a velocity profile, wherein the velocity profile comprises at least an acceleration component and a coast component. The driving current is adjusted in response to the comparison so that the velocity of the VCM substantially follows the velocity profile.