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Virtual Reality (VR) technology has advanced to include eye-tracking, allowing novel research, such as investigating how our visual system coordinates eye movements with changes in perceptual depth. The purpose of this study was to examine whether eye tracking could track perceptual depth changes during a visual discrimination task. We derived two depth-dependent variables from eye tracker data: eye vergence angle (EVA) and interpupillary distance (IPD). As hypothesized, our results revealed that shifting gaze from near-to-far depth significantly decreased EVA and increased IPD, while the opposite pattern was observed while shifting from far-to-near. Importantly, the amount of change in these variables tracked closely with relative changes in perceptual depth, and supported the hypothesis that eye tracker data may be used to infer real-time changes in perceptual depth in VR. Our method could be used as a new tool to adaptively render information based on depth and improve the VR user experience.