Japanese encephalitis virus (JEV) is a neurotropic flavivirus that is the causative agent of a major mosquito-borne encephalitis in the world. Evasion of peripheral immune system facilitates the entry of the virus into the central nervous system (CNS) where it causes extensive neuronal inflammatory damage that leads to death or severe neuropschychiatric sequel in survivors. It has been proposed that after entry into the body, the virus is carried into the CNS by peripheral immune cells that act as Trojan horses. In this study we investigate whether macrophages can be considered as such a Trojan horse. We also investigate the role of minocycline, a synthetic tetracycline, in such processes. Minocycline has been found to be broadly protective in neurological disease models featuring inflammation and cell death but there has been no report of it having any modulatory role in peripheral macrophage-mediated immune response against viral infection. Persistence of internalized virus within macrophages was visualized by immunofluorescent staining. Cytotoxicity assay revealed that there was no significant cell death after 24 h and 72 h infection with JEV. Proinflammatory cytokine levels were elevated in cells that were infected with JEV but it was abrogated following minocycline treatment. Reactive oxygen species level was also increased after JEV infection. Nitric oxide level was found to increase after 72 h post infection but remained unchanged after 24h. The cellular levels of signaling molecules such as PI3 kinase, phophoAkt and phospho p38MAP kinase were found to be altered after JEV infection and minocycline treatment. JEV infection also affected the VEGF-MMP pathway. Increased activity of MMP-9 was detected from JEV-infected macrophage culture supernatants after 72 h; minocycline treatment resulted in reduced activity. Thus it seems that minocycline dampens peripheral immune reactions by decreasing proinflammatory cytokine release from infected macrophages and the virus survives within macrophages long enough to be carried into the CNS, even though minocycline inhibits cell survival.