Recent fMRI studies have found that distinct neural systems may mediate perceptual category learning under implicit and explicit learning conditions. In these previous studies, however, different stimulus-encoding processes may have been associated with implicit versus explicit learning. The present design was aimed at decoupling the influence of these factors on the recruitment of alternate neural systems. Consistent with previous reports, following incidental learning in a dot-pattern classification task, participants showed decreased neural activity in occipital visual cortex (extrastriate region V3, BA 19) in response to novel exemplars of a studied category compared to members of a foil category, but did not show this decreased neural activity following explicit learning. Crucially, however, our results show that this pattern was primarily modulated by aspects of the stimulus-encoding instructions provided at the time of study. In particular, when participants in an implicit learning condition were encouraged to evaluate the overall shape and configuration of the stimuli during study, we failed to find the pattern of brain activity that has been taken to be a signature of implicit learning, suggesting that activity in this area does not uniquely reflect implicit memory for perceptual categories but instead may reflect aspects of processing or perceptual encoding strategies.