Eye-tracking methods may allow the online monitoring of cognitive processing during visual duration perception tasks, where participants are asked to estimate, discriminate, or compare time intervals defined by visual events like flashing circles.However, and to our knowledge, attempts to validate this possibility have remained inconclusive so far, and results remain focused on offline behavioral decisions made after stimulus appearance. This paper presents an eye-tracking protocol for exploring the cognitive processes preceding behavioral responses in an interval comparison task, where participants viewed two consecutive intervals and had to decide whether it speeded up (first interval longer than second) or slowed down (second interval longer).Our main concern was disentangling oculomotor responses to the visual stimulus itself from correlates of duration related to judgments. To achieve this, we defined three consecutive time windows based on critical events: baseline onset, the onset of the first interval, the onset of the second interval, and the end of the stimulus. We then extracted traditional oculomotor measures for each (number of fixations, pupil size) and focused on time-window-related changes to separate the responses to the visual stimulus from those related to interval comparison per se. As we show in the illustrative results, eye-tracking data showed significant differences that were consistent with behavioral results, raising hypotheses on the mechanisms engaged. This protocol is embryonic and will require many improvements, but it represents an important step forward in the current state of art.