A disk drive is disclosed comprising a disk having a plurality of tracks, a head actuated over the disk, and a voice coil motor for seeking the head from a first track to a second track. A first seek time is computed corresponding to a first seek profile, and second seek time is computed which is greater than the first seek time. A second seek profile is computed in response to the first seek time, the second seek time, and a scaling factor that accounts for a back EMF voltage generated by the voice coil motor. The voice coil motor is then controlled according to the second seek profile to seek the head from the first track to the second track.