The maintenance of immune homeostasis requires regulatory T cells (T-reg cells). Here we found that T-reg cell-specific ablation of Ubc13, a Lys63 (K63)-specific ubiquitin-conjugating enzyme, caused aberrant T cell activation and autoimmunity. Although Ubc13 deficiency did not affect the survival of T-reg cells or expression of the transcription factor Foxp3, it impaired the in vivo suppressive function of T-reg cells and rendered them sensitive to the acquisition of T helper type 1 (T(H)1) cell-and interleukin 17 (IL-17)-producing helper T (T(H)17) cell-like effector phenotypes. This function of Ubc13 involved its downstream target, the kinase IKK. The Ubc13-IKK signaling axis controlled the expression of specific T-reg cell effector molecules, including IL-10 and SOCS1. Collectively, our findings suggest that the Ubc13-IKK signaling axis regulates the molecular program that maintains T-reg cell function and prevents T-reg cells from acquiring inflammatory phenotypes.