Severe combined immunodeficiency (SCID) is an inherited disease with profoundly defective T cells, B cells, and natural killer (NK) cells. X-linked SCID (X-SCID) is its most common form. In this report, we describe a 4-month-old male with X-SCID who presented invagination and also showed hemophagocytic lymphohistiocytosis (HLH). The patient was admitted to our hospital with fever, cough, vomiting, monoliasis, and hepatosplenomegaly in postoperative period at the age of 3 months. The laboratory finding revealed no detectable T cells and hypogammaglobulinemia despite normal B-cell counts. Diagnosis of X-SCID was established by DNA analysis of the interleukin (IL)-2 receptor gamma chain gene ( IL2RG); namely, we detected the novel mutation in the splice-site of exon 5 (c.595-1G>T). The patient died due to infection at the age of 4 months. Also, this case is the first report that describes the patient with X-SCID with presented invagination.