JAK-STAT signaling pathway is an important cytokine signaling transduction pathway. Many monogenic loss-of-function or gain-of-function mutations in this pathway can cause inborn errors of immunity (IEI). Autoimmune diseases are caused by polygenic and different factors.The etiology of the disease is complex and diverse. The over-activation of JAK-STAT signaling pathway plays a significant role in the pathogenesis of autoimmune diseases. In this article, we summarize the mechanism of the JAK-STAT pathway and its role in the occurrence and development of IEI and autoimmune diseases, suggesting that the hyperactivation of JAK-STAT pathway having connection with IEI and autoimmune diseases. Meanwhile, we hope to make IEI a good model to study the pathogenesis of autoimmune diseases and to provide new ideas and directions for the clinical treatment of autoimmune diseases.