There is paucity of studies on the role of glutamate excitotoxicity in cell damage in Japanese encephalitis. In this study the glutamate levels and its NMDA receptors, and oxidative stress markers in different brain regions have been evaluated and correlated with neurobehavioral changes at different time points. Twelve day old Wistar rats were inoculated with 3×106pfu/ml intracerebrally. The neurobehavioral effects were evaluated by spontaneous locomotor activity (SLA), grip strength and rota rod test on 10, 33 and 48days post inoculation (dpi). Glutamate level was evaluated by enzyme linked immunosorbent assay, mRNA gene expression of ionotropic glutamate receptors N-methyl d-aspartate (NMDA) receptor 1, 2A and 2B (NR1, NR2A and NR2B) were evaluated by real time PCR. Malondialdehyde (MDA), glutathione (GSH) and glutathione peroxidase (GPx) levels were measured by spectrophotometer in different brain regions of JEV infected rats on 10, 33 and 48dpi. There was significant increase in motor deficit, grip strength and decreased locomotor activity on 10 and 33dpi. Glutamate levels were increased in thalamus, midbrain, frontal cortex, striatum and cerebellum on 10 and 33dpi and were followed by a recovery on 48dpi. Glutamate NMDR receptors NR1, NR2A and NR2B were reduced in thalamus, midbrain, frontal cortex, striatum and cerebellum on 10dpi which was followed by recovery after 33dpi. A significant increase in MDA level in thalamus, midbrain, frontal cortex, striatum and cerebellum was noted on 10 and 33dpi. The antioxidant GSH and GPx were significantly reduced in these brain regions on 10 and 33dpi. Glutamate, MDA, GSH and GPx correlated in different brain regions as the disease progress. Increased Glutamate level may be related to oxidative stress and may be responsible for behavioral alterations in rat model of Japanese encephalitis.