The immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is a rare genetic disease characterized by multiple immune disorders. Different mutations of the FOXP3 gene may lead to distinct clinical manifestations. Here, we present a rare case of IPEX syndrome caused by a novel variant of FOXP3. Clinical manifestations include autoimmune hemolysis, bronchiectasis, diarrhea, and proteinuria but without diabetes or other endocrine disorders. The diagnosis of IPEX syndrome was confirmed by whole-exon sequencing. Supportive treatment did not ameliorate the patient's symptoms, while immunosuppressive therapy showed a promising efficacy. The patient we reported will improve the understanding of renal manifestations in IPEX syndrome.