Herein, we present a case of isolated extramedullary relapse of CBFA2T3::GLIS2-positive AMKL after a second allogeneic hematopoietic stem cell transplantation (allo-HSCT) in a 3.5-year-old girl who was misdiagnosed with secondary Ewing sarcoma. Here, GLIS2 is linked to Ewing sarcoma.