The activation of the innate immune system induces the production of blood-borne proinflammatory cytokines like interleukin-1β (IL-1β), which in turn triggers brain-mediated adaptative responses referred to as sickness behaviour. These responses involve the modulation of neural networks in key regions of the brain. The nucleus tractus solitarius (NTS) of the brainstem is a key nucleus for immune-to-brain signalling. It is the main site of termination of vagal afferents and is adjacent to the area postrema, a circumventricular organ allowing blood-borne action of circulating IL-1β. Although it is well described that IL-1β activates cerebral endothelial and glial cells, it is still unknown if and how IL-1β or downstream-synthesized molecules impact NTS synaptic function. In this study we report that IL-1β did not modulate NTS synaptic transmission per se, whereas prostaglandin E2 (PGE2), which is produced downstream of IL-1β, produced opposite effects on spontaneous and evoked release. On the one hand, PGE2 facilitated glutamatergic transmission between local NTS neurons by enhancing the frequency of spontaneous excitatory postsynaptic currents through a presynaptic receptor different from the classical EP1–4 subtypes. On the other hand, PGE2 also depressed evoked excitatory input from vagal afferent terminals through presynaptic EP3 receptors coupled to G-proteins linked to adenylyl cyclase and protein kinase A activity. Our data show that IL-1β-induced PGE2 can modulate evoked and spontaneous release in the NTS differentially through different mechanisms. These data unravel some molecular mechanisms by which innate immune stimuli could signal to, and be integrated within, the brainstem to produce central adaptative responses.