Herein, we describe a case of highly refractory AML with recurrent cytogenetic abnormality t(6;9) and the FMS-like tyrosine kinase 3 gene (FLT3) internal tandem duplication (ITD) mutation and highlight the need for improved strategies to harness the immunotherapeutic benefits of HCT in conjunction with targetable agents. Here, FLT3 is linked to acute myeloid leukemia.