A data storage device is disclosed comprising an elevator actuator configured to actuate a head along an axial dimension, and a position sensor configured to generate a sinusoidal sensor signal representing a position of the head along the axial dimension, wherein the position sensor comprises a sensor element and an encoder strip comprising a pattern having at least one region that causes a disturbance in the sinusoidal sensor signal. The elevator actuator is controlled to move the head in a first direction along the axial dimension to detect the disturbance in the sinusoidal sensor signal, and when the disturbance in the sinusoidal signal is detected, the elevator actuator is controlled to move the head in a second direction along the axial dimension opposite the first direction in order to measure a zero crossing of the sinusoidal sensor signal.