How do the neural representations underlying category learning change as skill develops? We examined perceptual category learning using a prototype learning task known to recruit a corticostriatal system including the posterior striatum, motor cortex, visual cortex, and intraparietal sulcus (IPS). Male and female human participants practiced categorizing stimuli as category members or nonmembers (A vs not-A) across 3 d, with fMRI data collected at the beginning and end. Univariate analyses found that corticostriatal activity in regions associated with habitual instrumental learning was recruited across both sessions, but activity in regions associated with goal-directed instrumental learning decreased from Day 1 to Day 3. Multivoxel pattern analysis (MVPA) indicated that after training, the trained category could be more easily decoded from the IPS when compared with a novel category. Representational similarity analysis (RSA) showed development of category representations in the IPS and motor cortex. In addition, RSA revealed evidence for category-related representations including prototype representation in the ventromedial prefrontal cortex which may reflect parallel development of schematic memory for the category structure. Overall, the results converge to show how performance of category decisions and representations of the category structure emerge after extensive training across the corticostriatal system underlying perceptual category learning.