Japanese encephalitis virus (JEV) enters the brain through two different ways and leads to infection of neurons and encephalitis. On the left, it is proposed that JEV or JEV-infected leucocytes (monocytes, dendritic cells, T cells) circulating in the blood infect endothelial cells of the brain capillaries. The endothelial cells, without being harmed by JEV, amplify and transmit JEV to pericytes, or even microglia cells or astrocytes that are in contact with the capillaries. Infected pericytes, microglia, and astrocytes amplify JEV and transmit it to other brain cells, including neurons, astrocytes, and microglia. On the right, JEV-infected T cells or monocytes circulating in the blood migrate through the choroid plexus into the ventricular space with its cerebrospinal fluid, and from there into the periventricular nervous tissue. There, microglia, astrocytes, and neurons are infected either by cell-to-cell contact, or by newly produced extracellular JEV virions. In the middle, JEV-infected neurons undergo eventually apoptosis. In addition, JEV-infected microglia and astrocytes produce inflammatory factors (TNFα, IL-1) that induce collateral damage resulting in apoptosis of non-infected neurons.