Disk drive measuring reader/writer gap by measuring fractional clock cycle over disk radius

A disk drive is disclosed comprising a disk, and a head actuated radially over the disk, wherein the head comprises a read element separated from a write element by a reader/writer gap. A disk-locked clock is synchronized to a rotation of the disk, wherein the disk-locked clock comprises a plurality of clock cycles, and the reader/writer gap spans a first number of the clock cycles comprising an integer of the clock cycles plus a fraction of one of the clock cycles. The fraction of one of the clock cycles is measured when the head is positioned at a first plurality of radial locations across the disk, and a second plurality of radial locations is estimated where the fraction substantially equals a full one of the clock cycles.