The proprioceptive sensory inputs from neurons in the mesencephalic trigeminal nucleus (MesV) to masseter motoneurons (MMNs) play an important role in regulating masseter muscle activity during mastication. Several histological studies have shown that serotonin (5-HT) fibers densely innervate both the MesV and the trigeminal motor nucleus. However, the functional roles of 5-HT in the regulation of the excitatory synaptic inputs from MesV afferents to MMNs remain to be clarified. Thus, using the whole-cell recording technique in brainstem slice preparations from juvenile Wistar rats aged between postnatal days 8 and 12, we examined the effects of 5-HT on the excitatory synaptic inputs from MesV afferents to MMNs. Bath application of 5-HT reduced the peak amplitude of excitatory postsynaptic potentials evoked in MMNs by electrical stimulation of the MesV afferents (eEPSPs), and this inhibitory effect of 5-HT on eEPSPs was replicated with the 5-HT1B receptor agonist CP-93129 but not by the 5-HT1A receptor agonist 8-OH-DPAT. Moreover, the 5-HT1B receptor antagonist SB-224289 but not the 5-HT1A receptor antagonist WAY-100635 antagonized the inhibitory effect of 5-HT on eEPSPs. CP-93129 increased the paired-pulse ratio and decreased the frequency of miniature excitatory postsynaptic currents (mEPSCs), while it did not alter the mEPSC amplitude. These results suggest that presynaptic 5-HT1B receptors are involved in the inhibition of the excitatory synaptic inputs from MesV afferents to MMNs. Such inhibition may regulate MesV afferent activity during mastication.