Japanese encephalitis virus (JEV), a member of Faviviridae, is one of the leading causes of encephalitis in South-East Asia with approximtely 3 billion people living in endemic areas. Around 30, 000 cases are reported each year, and of these 30% result in fatality. The survivors of JE mostly have motor deficits, severe cognitive deficts, behavioral problems and neurological sequel which can be attributed to impaired neurogenesis pattern in the adult brain. JEV is an established neurotrpic virus and both direct as well as indirect microglial mediated neuronal killing has been observed. In this study, we have investigated whether JEV is capable of infecting the neural stem cells (NSCs) in the neurogenic areas of the brain and alter the fate of these cells. These multipotential stem cells have the ability to multiply and repopulate the brain following any neuronal loss in cases of central nervous system (CNS) injuries or insults. We report here that JEV indeed depletes the proliferating NSC population in the brain. Interestingly, the loss in NSCs was not a result of cell death or apoptosis induced by JE, rather the NSPCs appeared to be resilient to this viral infection. The virus however harbours in these cells and in the long run, decrases the proliferative ability of the NSCs. With progressive infection, cell cycle arrest in the NSCs accompanied with the decrease in the levels of various mitogenic signals has been observed. This arrest in cell cycling evetually culminates in a diminished NSC pool in the surviors of JE.