POLE codes for DNA polymerase epsilon (Pol ε) and variants of Pol ε catalytic subunit 1 can be pathogenic. We recently reported a novel POLE gene variant (p.[D1131fs];[T1891del]) which leads to bone marrow failure in two Japanese sisters. Here, we describe the successful course of hematopoietic stem cell transplantation of these two sisters. Both cases were born with congenital anemia and remained transfusion dependent. Their bone marrow showed gradually proceeding trilineage dysplasia. They both underwent HCT from an unrelated bone marrow donor and successfully achieved engraftment. Ten and eight years have passed respectively, and they are doing well without transfusion.