Disk drive adjusting fly height when calibrating head/disk contact

A disk drive is disclosed comprising a disk having a plurality of tracks, and a head actuated over the disk. The disk drive further comprises control circuitry including a fly height actuator. A fly height map is measured for at least one track. A constant FHC signal applied to the fly height actuator is adjusted to decrease an average fly height of the head. After decreasing the average fly height of the head, a fluctuating fly height control (FHC) signal is applied to the fly height actuator to adjust a fly height of the head in response to the fly height map. When the head contacts the disk, an operating FHC signal is determined. The operating FHC signal is applied to the fly height actuator while executing at least one of a read and write operation.