Aire-expressing medullary thymic epithelial cells (mTECs) play a key role in preventing autoimmunity by expressing tissue-restricted antigens to help purge the emerging T cell receptor repertoire of self-reactive specificities. Here we demonstrate a novel role for a CD4⁺3⁻ inducer cell population, previously linked to development of organized secondary lymphoid structures and maintenance of T cell memory in the functional regulation of Aire-mediated promiscuous gene expression in the thymus. CD4⁺3⁻ cells are closely associated with mTECs in adult thymus, and in fetal thymus their appearance is temporally linked with the appearance of Aire⁺ mTECs. We show that RANKL signals from this cell promote the maturation of RANK-expressing CD80⁻Aire⁻ mTEC progenitors into CD80⁺Aire⁺ mTECs, and that transplantation of RANK-deficient thymic stroma into immunodeficient hosts induces autoimmunity. Collectively, our data reveal cellular and molecular mechanisms leading to the generation of Aire⁺ mTECs and highlight a previously unrecognized role for CD4⁺3⁻RANKL⁺ inducer cells in intrathymic self-tolerance.