During Pavlovian conditioning the expression of a conditioned response is typically taken as evidence that an association between a conditioned stimulus (CS) and an unconditioned stimulus (UCS) has been formed. However, learning-related changes in the unconditioned response (UCR) produced by a predictable UCS can also develop. Learning-related reductions in UCR magnitude are often referred to as UCR diminution. In the present study, we examined UCR diminution in the functional magnetic resonance imaging (fMRI) signal by pairing supra- and sub-threshold CS presentations with a UCS. UCR diminution was observed within several brain regions associated with fear learning and memory including the insula, inferior parietal lobe, ventromedial prefrontal cortex (PFC), dorsomedial PFC, and dorsolateral PFC. CS perception appeared to mediate UCR diminution within the ventromedial PFC and posterior cingulate cortex. UCRs within these regions were larger when the UCS followed an unperceived compared to a perceived CS. UCS expectancies appeared to modulate UCRs within the dorsomedial PFC, dorsolateral PFC, insula, and inferior parietal lobe. Activity within these regions showed an inverse relationship with participants' UCS expectancies, such that as UCS expectancy increased UCR magnitude decreased. In addition, activity within the dorsomedial PFC, dorsolateral PFC, and insula showed a linear relationship with unconditioned skin conductance response (SCR) expression. These findings demonstrate UCR diminution within the fMRI signal, and suggest that UCS expectancies modulate prefrontal cortex responses to aversive stimuli. In turn, prefrontal cortex activity appears to modulate the expression of unconditioned SCRs.