Abstract The thymus is a target of multiple pathogens. How the immune system responds to thymic infection is largely unknown. Despite being considered an immune-privileged organ, we detect a mycobacteria-specific T cell response in the thymus following dissemination of Mycobacterium avium or Mycobacterium tuberculosis. This response includes proinflammatory cytokine production by mycobacteria-specific CD4+ and CD8+ T cells, which stimulates infected cells and controls bacterial growth in the thymus. Importantly, the responding T cells are mature peripheral T cells that recirculate back to the thymus. The recruitment of these cells is associated with an increased expression of Th1 chemokines and an enrichment of CXCR3+ mycobacteria-specific T cells in the thymus. Finally, we demonstrate it is the mature T cells that home to the thymus that most efficiently control mycobacterial infection. Although the presence of mature T cells in the thymus has been recognized for some time, to our knowledge, these data are the first to show that T cell recirculation from the periphery to the thymus is a mechanism that allows the immune system to respond to thymic infection. Maintaining a functional thymic environment is essential to maintain T cell differentiation and prevent the emergence of central tolerance to the invading pathogens.