A fly height control system comprises a measurement circuit that receives M pulses that are based on a predetermined pattern stored on a storage medium and that determines a first amplitude and a second amplitude for each of the M pulses, where M is an integer greater than one. The first amplitude is determined at a first time and the second amplitude is determined at a second time that is different than the first time. A calculation circuit determines a distance between a head and a storage medium based on a function of the first amplitudes for the M pulses and the second amplitudes for the M pulses. A head controller controls the head based on the distance determined by the calculation circuit.