A disk drive is disclosed comprising a disk, a head actuated over the disk, and control circuitry operable to estimate a fly height of the head by tuning a phase locked loop (PLL) in response to a fly height capacitance. In one embodiment, the PLL comprises a resistive component having a second terminal coupled to the fly height capacitance, a variable oscillator operable to generate a first oscillating signal applied to a first terminal of the resistive component to generate a second oscillating signal at the second end of the resistive component, and a phase detector operable to generate a control signal by comparing a phase of the first oscillating signal to a phase of the second oscillating signal. The control signal is applied to the variable oscillator to adjust a frequency of the first oscillating signal.