Perceptually similar stimuli often predict vastly different outcomes, requiring the brain to maintain specific associations in the face of potential ambiguity. This could be achieved either through local changes in stimulus representations, or through modulation of functional connections between stimulus-coding and outcome-coding regions. Here we test these competing hypotheses using classical conditioning of perceptually similar odours in the context of human fMRI. Pattern-based analyses of odour-evoked fMRI activity reveal that odour category, identity and value are coded in piriform (PC), orbitofrontal (OFC) and ventromedial prefrontal (vmPFC) cortices, respectively. However, we observe no learning-related reorganization of category or identity representations. Instead, changes in connectivity between vmPFC and OFC are correlated with learning-related changes in value, whereas connectivity changes between vmPFC and PC predict changes in perceived odour similarity. These results demonstrate that dissociable neural pathways support associative and perceptual representations of sensory stimuli.