Post-tetanic Ca2+ release from mitochondria produces presynaptic residual calcium, which contributes to post-tetanic potentiation. The loss of mitochondria-dependent post-tetanic potentiation is one of the earliest signs of Alzheimer's model mice. Post-tetanic potentiation at intracortical synapses of medial prefrontal cortex has been implicated in working memory. Although mitochondrial contribution to post-tetanic potentiation differs depending on synapse types, it is unknown which synapse types express mitochondria-dependent post-tetanic potentiation in the medial prefrontal cortex. We studied expression of mitochondria-dependent post-tetanic potentiation at different intracortical synapses of the rat medial prefrontal cortex. Post-tetanic potentiation occurred only at intracortical synapses onto layer 5 corticopontine cells from commissural cells and L2/3 pyramidal neurons. Among post-tetanic potentiation-expressing synapses, L2/3-corticopontine synapses in the prelimbic cortex were unique in that post-tetanic potentiation depends on mitochondria because post-tetanic potentiation at corresponding synapse types in other cortical areas was independent of mitochondria. Supporting mitochondria-dependent post-tetanic potentiation at L2/3-to-corticopontine synapses, mitochondria-dependent residual calcium at the axon terminals of L2/3 pyramidal neurons was significantly larger than that at commissural and corticopontine cells. Moreover, post-tetanic potentiation at L2/3-corticopontine synapses, but not at commissural-corticopontine synapses, was impaired in the young adult Alzheimer's model mice. These results would provide a knowledge base for comprehending synaptic mechanisms that underlies the initial clinical signs of neurodegenerative disorders.