The current understanding of the neuromodulatory role of the median raphe nucleus (MRN) is primarily based on its putative serotonergic output. However, a significant proportion of raphe neurons are glutamatergic. The present study investigated how glutamatergic MRN input modulates the medial prefrontal cortex (mPFC), a critical component of the fear circuitry. Our studies show that VGLUT3-expressing MRN neurons modulate VGLUT3- and somatostatin-expressing neurons in the mPFC. Consistent with this modulation of mPFC GABAergic neurons, activation of MRN (VGLUT3) neurons suppresses mPFC pyramidal neuron activity and attenuates fear memory in female but not male mice. In agreement with these female-specific effects, we observed sex differences in glutamatergic transmission onto MRN (VGLUT3) neurons and mPFC (VGLUT3) neuron-mediated dual release of glutamate and GABA. Thus, our results demonstrate a cell type-specific modulation of the mPFC by MRN (VGLUT3) neurons and reveal a sex-specific role of this neuromodulation in mPFC synaptic plasticity and fear memory.