A system and method accurately clocks write data to the discrete data blocks in a patterned media disk drive. The precise time intervals between successive timing marks in the data tracks are measured by a timing mark detector that counts the integer number of write clock cycles between successive timing marks and the fractional part of a write clock cycle by detecting the phase difference between a timing mark and a reference signal. The resulting timing error is output to a write clock compensator. The write clock is capable of generating equally spaced primary phases and phases intermediate the primary phases. The compensator includes a phase rotator that controls which write clock phase is selected for output. The value in a phase register of the compensator is used to control the phase rotator to advance or retard the write clock phase, and thus to adjust its frequency and phase so as to be synchronized for writing to the data blocks.