Foxp3-expressing regulatory T (Treg) cells protect against systemic autoimmunity. However, little is known about the significance of Treg cells in inflammation-experienced tissues. Here, we use an experimental autoimmune encephalomyelitis model and show that Treg cells accumulate and persist in the central nervous system (CNS) long after the resolution of the bulk of the inflammatory infiltrate. CNS-specific depletion of postinflammatory Treg cells, but not systemic depletion of Treg cells, results in autoimmune inflammatory flares in the CNS by residual local effector T cells. Expression of the NAD-consuming ectoenzyme CD38 is crucial for the functional adaptation of postinflammatory CNS Treg cells to a stressful microenvironment, in which access to interleukin-2 (IL-2) is limited. CD38 counteracts ADP-ribosylation of the IL-2 receptor and thus maintains its high sensitivity to IL-2. This fully functional high-affinity IL-2 receptor prevents the loss of tissue-resident antigen-specific Treg cells. These 'stress-tolerant' CNS Treg cells impede the collapse of immune homeostasis in the CNS once acute inflammation is controlled.