Binary classification, an act of sorting items into two classes by setting a boundary, is biased by recent history. One common form of such bias is repulsive bias, a tendency to sort an item into the class opposite to its preceding items. Sensory-adaptation and boundary-updating are considered as two contending sources of the repulsive bias, yet no neural support has been provided for either source. Here, we explored human brains of both men and women, using functional magnetic resonance imaging (fMRI), to find such support by relating the brain signals of sensory-adaptation and boundary-updating to human classification behavior. We found that the stimulus-encoding signal in the early visual cortex adapted to previous stimuli, yet its adaptation-related changes were dissociated from current choices. Contrastingly, the boundary-representing signals in the inferior-parietal and superior-temporal cortices shifted to previous stimuli and covaried with current choices. Our exploration points to boundary-updating, rather than sensory-adaptation, as the origin of the repulsive bias in binary classification.SIGNIFICANCE STATEMENTMany animal and human studies on perceptual decision-making have reported an intriguing history effect called “repulsive bias,” a tendency to classify an item as the opposite class of its previous item. Regarding the origin of repulsive bias, two contending ideas have been proposed: “bias in stimulus representation because of sensory adaptation” versus “bias in class-boundary setting because of belief updating.” By conducting model-based neuroimaging experiments, we verified their predictions about which brain signal should contribute to the trial-to-trial variability in choice behavior. We found that the brain signal of class boundary, but not stimulus representation, contributed to the choice variability associated with repulsive bias. Our study provides the first neural evidence supporting the boundary-based hypothesis of repulsive bias.