The molecular mechanisms of antiviral innate immune reactions in brain microvascular endothelial cells remain unclear. Interferon (IFN)-induced transmembrane protein 1 (IFITM1) and Myxovirus resistance protein 1 (MX1), the members of IFN-stimulated genes, are known as antiviral molecules. IFITM1 inhibits virus entry into host cell cytoplasm, whereas MX1 antagonizes virus replication. Here we observed that IFITM1 and MX1, and a proinflammatory cytokine IL-6 expression was induced by polyinosinic-polycytidylic acid (poly IC) in hCMEC/D3 human brain microvascular endothelial cells. Poly IC-induced IFITM1 and MX1 expression were decreased by NF-κB inhibitor SN50, IFN regulatory factor 3 inhibitor MRT67307 and human type I IFN neutralizing antibody mixture. These findings suggest that IFITM1 and MX1 may help protect the brain from viruses.