Japanese encephalitis virus (JEV) remains a leading cause of encephalitis, globally, which continues to grow in importance despite the availability of a vaccine. Viral entry into the brain is via the blood-brain barrier (BBB), and inflammation at the BBB is a final common pathway in many brain infections. However, the exact mechanisms of JEV entry into the brain and the contribution of BBB inflammation to this are incompletely understood. We established a BBB model using human brain endothelial cells (HBECs) and astrocytes. BBB model was inoculated from the luminal side and the effects of JEV on the BBB were investigated. JEV infected HBECs with limited active replication, before crossing the BBB and replicating in astrocytes. Control of viral replication by HBECs was associated with a significant increase in permeability, and with elevation of many host mediators, including cytokines, chemokines, cellular adhesion molecules, and matrix metalloproteases. Several mediators were significantly increased in the luminal side compared to the abluminal side, and correlated with an increased permeability. Treatment with dexamethasone led to a significant reduction in the release of IL6, CCL5 and CXCL10 from the luminal side with a reduction in BBB disruption. The results are consistent with the hypothesis that JEV infection of the vascular endothelium triggers the production of a range of host mediators, which control viral replication but disrupt BBB integrity thus allowing virus entry into the brain. Dexamethasone treatment controlled this host response, and limited BBB disruption in the model, supporting a re-investigation of its use therapeutically in viral encephalitis. In addition, a flow-based human BBB model that mimics the blood flow in brain capillaries is currently being optimised to study JEV and other flavivirus interactions with the BBB.