Immune tolerance is maintained in lymphoid organs (LOs). Despite the presence of complex immune cell networks in non-LOs, it is unknown whether self-tolerance is maintained in these tissues. We developed a technique to restrict genetic recombination to regulatory T cells (T _regs ) only in skin. Selective depletion of skin T _regs resulted in T cell–mediated inflammation of hair follicles (HFs). Suppression did not rely on CTLA-4, but instead on high-affinity interleukin-2 (IL-2) receptor expression by skin T _regs , functioning exclusively in a cell-extrinsic manner. In a novel model of HF stem cell (HFSC)–driven autoimmunity, we reveal that skin T _regs immunologically protect the HFSC niche. Finally, we used spatial transcriptomics to identify aberrant IL-2 signaling at stromal-HF interfaces in a rare form of human alopecia characterized by HFSC destruction and alopecia areata. Collectively, these results reveal the fundamental biology of T _regs in skin uncoupled from the systemic pool and elucidate a mechanism of self-tolerance.