A disk drive is disclosed comprising a disk, a head actuated over the disk, and control circuitry operable to generate a fly height control signal. A fly height of the head is measured, and the measured fly height is combined with a target fly height and a feedforward signal, wherein the feedforward signal is generated according to: a.sub.1cos(2.pi.n.sub.1k/N)+b.sub.1sin(2.pi.n.sub.1k/N) where a.sub.1 and b.sub.1 are coefficients and 2.pi.n.sub.1k/N represents a frequency of a repeatable disturbance in the fly height of the head.