Adaptive behavior involves interactions between systems regulating Pavlovian and instrumental control of actions. Here, we present the first investigation of the neural mechanisms underlying aversive Pavlovian-instrumental transfer using fMRI in humans. Recent evidence indicates that these Pavlovian influences on instrumental actions are action-specific: Instrumental approach is invigorated by appetitive Pavlovian cues but inhibited by aversive Pavlovian cues. Conversely, instrumental withdrawal is inhibited by appetitive Pavlovian cues but invigorated by aversive Pavlovian cues. We show that BOLD responses in the amygdala and the nucleus accumbens were associated with behavioral inhibition by aversive Pavlovian cues, irrespective of action context. Furthermore, BOLD responses in the ventromedial prefrontal cortex differed between approach and withdrawal actions. Aversive Pavlovian conditioned stimuli modulated connectivity between the ventromedial prefrontal cortex and the caudate nucleus. These results show that action-specific aversive control of instrumental behavior involves the modulation of fronto-striatal interactions by Pavlovian conditioned stimuli.