A disk drive is disclosed comprising a disk and a head actuated over the disk, the head comprising a fly height actuator (FHA). The disk drive further comprises control circuitry including disk access circuitry, wherein during a calibration operation, the disk access circuitry is configured into a calibration mode that increases a heating of the head, and a fly height of the head is measured periodically to generate periodic fly height measurements that vary due to the heating of the head. A dynamic fly height (DFH) write profile is generated based on the periodic fly height measurements. During a write operation, the disk access circuitry is configured into a write mode and a DFH control signal is generated and applied to the FHA based on the DFH write profile.