Matrix metalloproteinases (MMPs) are widely implicated in modulating blood brain barrier (BBB) integrity and affect the entry of peripheral immune cells into the central nervous system (CNS). The expression of MMPs is tightly regulated at the level of gene transcription, conversion of pro-enzyme to active MMPs and by the action of tissue inhibitors of metalloproteinases (TIMP). The crucial role of MMPs in inflammation indicates that perturbation of the MMP/TIMP balance decisively plays an important role in pathogenesis during viral encephalitis. The study was performed to evaluate the production of MMP-2, MMP-7, MMP-9, TIMP-1 and TIMP-3 in the sera of JEV i.e. GP 78668A (GP-78) infected BALB/c mouse model of encephalitis and gel zymography was performed for MMP-2 and MMP-9 activities. The estimation of MMP-2, MMP-7, MMP-9, TIMP-1, and TIMP-3 in JEV-infected mouse serum was analyzed by ELISA along with brain histopathology and immunohistochemistry. Evan’s blue dye exclusion test was done to check the BBB integrity. Gelatin gel zymography was performed for MMP-2 and MMP-9 activities. We noticed an upregulated expression of MMPs in the sera of virus infected groups compared to controls at different days post inoculation (dpi). Post hoc analysis between days also reveals significant increase (p