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Prominent accounts of Pavlovian conditioning successfully approximate the frequency and intensity of conditioned responses under the assumption that learning is exclusively model-free; that animals do not develop a cognitive map of events. However, these model-free approximations fall short of comprehensively capturing learning and behavior in Pavlovian conditioning. We therefore performed multivoxel pattern analysis of high-resolution functional MRI data in human participants to test for the encoding of stimulus-stimulus associations that could support model-based computations during Pavlovian conditioning. We found that dissociable sub-regions of the striatum encode predictions of stimulus-stimulus associations and predictive value, in a manner that is directly related to learning performance. Activity patterns in the orbitofrontal cortex were also found to be related to stimulus-stimulus as well as value encoding. These results suggest that the brain encodes model-based representations during Pavlovian conditioning, and that these representations are utilized in the service of behavior.