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In binocular rivalry, two incompatible inputs are presented separately to the two eyes, causing subjects to alternate between two perceptual interpretations. These percept switches engage a large frontoparietal network, accompanied by large pupil dilations. It is unclear whether these measured functional MRI (fMRI) and pupil responses relate to neural processing causing the switches, or constitute the brain’s response to the switches. The temporal dynamics with which subjects switch between the two interpretations are determined by catecholaminergic neuromodulatory systems and these dynamics should be reflected in pupil size. We simultaneously recorded pupil dilation and fMRI during binocular rivalry, and show a biphasic pupil response around the time of a percept switch. The strength of a transient pupil dilation after the behavioral response reflects the temporal predictability of the switch. We also find a marked pupil constriction before the behavioral response. Surprisingly, the amplitude of this constriction predicts the duration of the subsequent percept several seconds in advance, implying that the pupil can be used as a proxy for two different neural mechanisms underpinning perceptual dynamics in ambiguous perception. Together with concurrent fMRI recordings, these results allow us to disambiguate between competing computational accounts of the ongoing inference process that shapes the dynamics of bistable perception.