Background: Transcobalamin (TC) is a carrier protein and it delivers vitamin B12 to the cellular TC receptor. TC II deficiency is a very rare disease and is life-threatening if left untreated. It is an Autosomal recessive disease and needs lifelong treatment. The clinical presentations are variable, started at early infancy, and sometimes mimic severe combined immunodeficiency or acute leukemia. It includes failure to thrive, diarrhea, anemia and or pancytopenia, hypotonia, developmental delay, and recurrent infection. Diagnosis of TC II deficiency is suspected based on clinical presentations with megaloblastic anemia, the elevation of plasma homocysteine, and urine methylmalonic acid level with a normal vitamin B12 and folate level. Molecular analysis of the TCN 2 gene is needed for confirmation of the diagnosis. Case Presentation: We present a case of 2 years old Saudi boy who was admitted to the hospital with a history of fever, recurrent chest infection, failure to thrive with diarrhea, and hypotonia, and his complete blood counts showed Pancytopenia. Though, normal vitamin B12 level and folate level, homocysteine, and urine methylmalonic acid lever were elevated. Peripheral smear and bone marrow aspiration and biopsy revealed Hypersegmented neutrophils and megaloblastic change.