Pupil size is modulated by various cognitive factors such as attention, working memory, mental imagery, and subjective perception. Previous studies examining cognitive effects on pupil size mainly focused on inducing or enhancing a subjective experience of brightness or darkness (for example by asking participants to attend to/memorize a bright or dark stimulus), and then showing that this affects pupil size. Surprisingly, the inverse has never been done; that is, it is still unknown what happens when a subjective experience of brightness or darkness is eliminated or strongly reduced even though bright or dark stimuli are physically present. Here, we aim to answer this question by using perceptual fading, a phenomenon where a visual stimulus gradually fades from visual awareness despite its continuous presentation. The study contains two blocks: Fading and Non-Fading. In the Fading block, participants were presented with black and white patches with a fuzzy outline that were presented at the same location throughout the block, thus inducing strong perceptual fading. In contrast, in the Non-Fading block, the patches switched sides on each trial, thus preventing perceptual fading. Participants covertly attended to one of the two patches, indicated by a cue, and reported the offset of one of a set of circles that are displayed on top. We hypothesized that pupil size will be modulated by covert visual attention in the Non-Fading block, but that this effect will not (or to a lesser extent) arise in the Fading block. We found that covert visual attention to bright/dark does modulate pupil size even during perceptual fading (Fading block), but to a lesser extent than when the perceptual experience of brightness/darkness is preserved (Non-Fading block). This implies that pupil size is always modulated by covert attention, but that the effect decreases as subjective experience of brightness or darkness decreases. In broader terms, this suggests that cognitive modulations of pupil size reflect a mixture of high-level and lower-level visual processing.