Gain-of-function mutations of the CKIT gene have been reported to specifically occur in core-binding factor (CBF) acute myeloid leukemia (AML) with a poor prognostic implication. Here we report a case of therapy-related AML with t(9;11)(p22;q23) who had CKIT mutation. A 48-year-old woman with breast cancer received partial mastectomy followed by 6 cycles of adjuvant chemotherapy and radiation therapy. At 28 months from the diagnosis of breast cancer, she was diagnosed as having AML with blasts 81% in bone marrow. Cytogenetic analysis revealed t(9;11)(p22;q23), and FISH showed 96.5% of MLL break-apart signals. RT-PCR study revealed MLL(11q23)/MLLT3(9p22) chimeric transcript. FLT3-ITD and NPM1 mutations were both negative. Unexpectedly, mutation analyses for CKIT identified D816Y mutation. The patient received induction chemotherapy and achieved complete remission at 1 month. To the best of our knowledge, this is the first report on CKIT mutation in therapy-related AML with MLL rearrangement.