In the central nervous system, the Japanese encephalitis virus can replicate only in neurons. The mechanism of the type of neurotropism was analyzed. The susceptibility to Japanese encephalitis virus infection in the rat brain was closely associated with neuronal immaturity. The initial specific binding of the virus to cells is one of the reasons for neurotropism of the Japanese encephalitis virus. The treatment of Japanese encephalitis virus infection with the neutralizing monoclonal antibody against the E protein did not inhibit the virus from binding to the cell surfaces, but strongly inhibited Japanese encephalitis virus-induced cell fusion and internalization of the virus into the host cells. One of the genome regions responsible for neuropathogenesis of the Japanese encephalitis virus was located on the E protein-coding region. The 138th amino acid of the E protein was important for neuropathogenesis expression of the Japanese encephalitis virus. The cell fusion activity of the E protein was closely correlated with neuropathogenesis of the virus.