To guide behavior, perceptual systems must operate on intrinsically ambiguous sensory input. Observers are usually able to acknowledge the uncertainty of their perception, but in some cases, they critically fail to do so. Here, we show that a physiological correlate of ambiguity can be found in pupil dilation even when the observer is not aware of such ambiguity. We used a well-known auditory ambiguous stimulus, known as the tritone paradox, which can induce the perception of an upward or downward pitch shift within the same individual. In two experiments, behavioral responses showed that listeners could not explicitly access the ambiguity in this stimulus, even though their responses varied from trial to trial. However, pupil dilation was larger for the more ambiguous cases. The ambiguity of the stimulus for each listener was indexed by the entropy of behavioral responses, and this entropy was also a significant predictor of pupil size. In particular, entropy explained additional variation in pupil size independent of the explicit judgment of confidence in the specific situation that we investigated, in which the two measures were decoupled. Our data thus suggest that stimulus ambiguity is implicitly represented in the brain even without explicit awareness of this ambiguity.