The reciprocal connectivity between the medial prefrontal cortex (mPFC) and the dorsal raphe nucleus (DR) is involved in mood control and resilience to stress. The infralimbic subdivision (IL) of the mPFC is the rodent equivalent of the ventral anterior cingulate cortex, which is intimately related to the pathophysiology/treatment of major depressive disorder (MDD). Boosting excitatory neurotransmission in the IL—but not in the prelimbic cortex, PrL—evokes depressive-like or antidepressant-like behaviors in rodents, which are associated with changes in serotonergic (5-HT) neurotransmission. We therefore examined the control of 5-HT activity by both of the mPFC subdivisions in anesthetized rats. The electrical stimulation of IL and PrL at 0.9 Hz comparably inhibited 5-HT neurons (53% vs. 48%, respectively). However, stimulation at higher frequencies (10–20 Hz) revealed a greater proportion of 5-HT neurons sensitive to IL than to PrL stimulation (86% vs. 59%, at 20 Hz, respectively), together with a differential involvement of GABAA (but not 5-HT1A) receptors. Likewise, electrical and optogenetic stimulation of IL and PrL enhanced 5-HT release in DR in a frequency-dependent manner, with greater elevations after IL stimulation at 20 Hz. Hence, IL and PrL differentially control serotonergic activity, with an apparent superior role of IL, an observation that may help to clarify the brain circuits involved in MDD.