A disk drive is disclosed including a disk having a plurality of tracks, wherein each track comprises a plurality of data sectors and a plurality of servo sectors. The disk drive further comprises a spindle motor for rotating the disk, and a head actuated radially over the disk, wherein the head comprises a dynamic fly height (DFH) heater. Control circuitry within the disk drive is operable to position the head over one of the tracks; determine a number of servo sectors to pass under the head before a target location over the track is reached, apply an initial amount of power to the DFH heater that is dependent at least in part on the determined number of servo sectors, and decrease the initially-applied amount of power applied to the DFH heater until a predetermined target power is reached.