Retrieval of fear extinction memory is associated with increased firing of neurons in the medial prefrontal cortex (mPFC). It is unknown, however, how extinction learning-induced changes in mPFC activity are relayed to target structures in the amygdala, resulting in diminished fear responses. Here, we show that fear extinction decreases the efficacy of excitatory synaptic transmission in projections from the mPFC to the basolateral nucleus of the amygdala (BLA), whereas inhibitory responses are not altered. In contrast, synaptic strength at direct mPFC inputs to intercalated neurons remains unchanged after extinction. Moreover, priming stimulation of mPFC projections induced heterosynaptic inhibition in auditory cortical inputs to the BLA. These synaptic mechanisms could contribute to the encoding of extinction memory by diminishing the ability of projections from the mPFC to drive BLA activity while retaining the ability of intercalated neurons to inhibit the output nuclei of the amygdala.