MHC Class II deficiency (also known as bare lymphocyte syndrome type II) is a rare primary immunodeficiency disorder inherited in an autosomal recessive fashion resulting from the absence of MHC class II molecules on the surface of immune cells. Here, we report a now 18-month-old male born to consanguineous Mexican-American parents who presented at four months with pneumocystis pneumonia, and was subsequently found to have a novel homozygous mutation in RFXANK leading to MHC Class II deficiency. He was successfully treated via hematopoietic stem cell transplantation from his matched sibling.