Various studies reported c-Fos expression in the neurons in the trigeminal sensory nuclear complex (TSNC) following experimental tooth movement, which implies pain transmission to the central nervous system. Meanwhile, MK-801, a noncompetitive antagonist of N-methyl- d-aspartate (NMDA) receptors, was shown to markedly reduce the expression of c-Fos in the trigeminal subnucleus caudalis (Vc) following noxious stimulation but to enhance c-Fos expression markedly in other brain regions, i.e., the neocortex, dorsal raphe and thalamic nuclei. In the present study, we examined the nature of c-Fos expression in the brainstem including the TSNC and midbrain following administration of MK-801 and/or experimental movement of the rat molars. Twelve hours after the beginning of experimental tooth movement, c-Fos was expressed bilaterally in the superficial laminae of Vc (Vc I/II), dorsomedial areas of the trigeminal subnucleus oralis (Vodm) and rostro-dorsomedial areas of the trigeminal subnucleus oralis (Vor) with the ipsilaterally dominant distribution, but hardly in the periaqueductal gray (PAG), dorsal raphe nucleus (DR) and Edinger–Westphal nucleus (EW). Intraperitoneal administration of MK-801 (0.03, 0.3 and 3.0 mg/kg) prior to the onset of experimental tooth movement reduced c-Fos in the TSNC (Vc I/II, Vodm and Vor) but increased it in the nucleus raphe magnus (NRM), ventrolateral PAG (vl PAG), DR and EW. These results highly emphasize that during experimental tooth movement, a blockade of NMDA receptors induces neuronal suppression in the TSNC but increases neuronal activity in the descending antinociceptive system including the NRM, vl PAG, DR and EW.