BK polyomavirus (PyV) establishes lifelong asymptomatic infections in the reno-urinary system of most humans. BKPyV-associated nephropathy is the leading infectious cause of kidney allograft loss. Using mouse PyV, a natural murine pathogen that also persists in the kidney, we define a dominant chemokine receptor-chemokine axis that directs T cell infiltration of the kidney. We found that CXCR6 was required for CD4+ and CD8+ T cells to be recruited to and retained in the kidney, respectively. Absence of CXCR6 impaired virus control in the kidney. The soluble form of CXCL16 was increased in kidneys of infected mice and in vivo CXCL16 neutralization reduced numbers of virus-specific CD8+ T cells infiltrating the kidney. In vivo administration of IL-12 upregulated CXCR6 expression on virus-specific CD8+ T cells, improved T cell recruitment to the infected kidney, and reduced virus levels. Notably, T cells in kidney biopsies from PyV-associated nephropathy patients express CXCR6 and transcriptional analysis shows significant upregulation of CXCR6 and CXCL16. These findings demonstrate the importance of the CXCR6-CXCL16 axis in regulating T cell responses in the kidney to PyV infection.