A disk drive is disclosed comprising a disk having a plurality of tracks, and a head actuated over the disk. Control circuitry heats the head in order to reduce a fly-height of the head, and computes a target servo sector to begin a preheat period. The control circuitry decreases the heat so that the fly-height is increased during at least part of a seek operation to seek the head from a first track to a second track. When the head reaches the target servo sector, the control circuitry increases the heat to decrease the fly-height during the preheat period.