Disk drive seeking with a fixed rate clock when crossing servo zones to facilitate zoned servo sectors

A disk drive is disclosed comprising a disk having a plurality of servo sectors defining a plurality of servo tracks that form a plurality of servo zones. The disk drive further comprises a head actuated radially over the disk for generating a read signal, and control circuitry operable to execute a seek operation. A fixed rate clock is generated, and a disk locked clock is generated and synchronized to the servo data rate of the servo zone the head is over. The disk locked clock is used to generate a servo timing window relative to a circumferential location of the head and the servo sectors. The control circuitry seeks the head from the first servo zone to the second servo zone, and switches to the fixed rate clock to generate the servo timing window while the head transitions from the first servo zone to the second servo zone.