A critical component of decision making is the ability to adjust criteria for classifying stimuli. fMRI and drift diffusion models were used to explore the neural representations of perceptual criteria in decision making. The specific focus was on the relative engagement of perceptual- and decision-related neural systems in response to adjustments in perceptual criteria. Human participants classified visual stimuli as big or small based on criteria of different sizes, which effectively biased their choices toward one response over the other. A drift diffusion model was fit to the behavioral data to extract estimates of stimulus size, criterion size, and difficulty for each participant and condition. These parameter values were used as modulated regressors to create a highly constrained model for the fMRI analysis that accounted for several components of the decision process. The results show that perceptual criteria values were reflected by activity in left inferior temporal cortex, a region known to represent objects and their physical properties, whereas stimulus size was reflected by activation in occipital cortex. A frontoparietal network of regions, including dorsolateral prefrontal cortex and superior parietal lobule, corresponded to the decision variables resulting from the downstream stimulus-criterion comparison, independent of stimulus type. The results provide novel evidence that perceptual criteria are represented in stimulus space and serve as inputs to be compared with the presented stimulus, recruiting a common network of decision regions shown to be active in other simple decisions. This work advances our understanding of the neural correlates of decision flexibility and adjustments of behavioral bias.