A disk drive is disclosed comprising a head actuated over a disk comprising a plurality of data tracks defined by servo sectors. The head comprises a laser operable to heat the disk while writing data to the disk and a fly height actuator operable to adjust a fly height of the head over the disk. When the head approaches a target data sector of a write command, the fly height of the actuator adjusts the fly height of the head to a target pre-heat fly height during a pre-heat interval. After the pre-heat interval and during a pre-laser interval, the fly height actuator increases the fly height of the head. After the pre-laser interval, a power applied to the laser is increased to heat the disk, wherein the pre-laser interval compensates for a protrusion transient of the head toward the disk due to increasing the power applied to the laser.