West Nile virus (WNV) is one of the most widespread, neuroinvasive flaviviruses transmitted by mosquitoes. In some, a severe immunopathological response progresses to acute lethal encephalitis. To elucidate the mechanism of immune pathogenesis, a detailed understanding of the immune response to WNV is needed.. We investigated responses of the draining lymph nodes (LN) of the CNS using non-draining peripheral LN as controls in viral encephalitis in an intranasal model of WNV infection. The expansion of leukocyte numbers in the cervical LN by up to 5-fold at the peak of infection on d7 p.i. suggest a critical role in the initiation of the adaptive anti-viral immune response to WNV. Dendritic cell (DC) populations increase 24h prior to B- and T-cell expansion at D3 p.i., potentially inducing and enhancing T-cell activation and clonal expansion. Although increased T-cell numbers in the cervical LN are due to some in situ proliferation, some are likely recruited from elsewhere. Indeed, although not previously studied, distinct changes occur in the mesenteric and inguinal LN, i.e., LN not associated with the CNS. These show a reduction of up to 50% in both CD4+ and CD8+ T-cell populations, with a significant upregulation of Ly6C on these cells, suggesting the acquisition of a migratory phenotype. Although numbers were unchanged, CD8α-DC of non-draining LN also showed significantly increased Ly6C expression, suggesting an inflammatory response in the non-draining LN. We hypothesise that these T-cells preferentially home to cervical LN and form part of the effector cell population in the adaptive immune response to WNV in the CNS. Further characterisation of this response will determine the kinetics of emigration of T-cells from these ‘non-draining’ LN and their specific contribution to the anti-viral immune response.