A 58-year-old man was diagnosed with accelerated phase chronic myelogenous leukemia (CML). He was treated with dasatinib and followed-up; 6 months later, he achieved a complete molecular response. Seventeen months after this therapy, he developed pancytopenia, and was examined. His diagnosis was Ph-negative acute myeloid leukemia (AML) with no karyotype abnormalities. He was administered two courses of induction chemotherapy, and during the first remission, he received allogeneic hematopoietic stem cell transplantation. Treatment with a tyrosine kinase inhibitor (TKI) achieved a successful outcome. However, approximately 10% of CML cases develop clonal cytogenetic changes in Ph-negative cells during TKI treatment, and rarely, cases of Ph-negative myelodysplastic syndrome or AML are reported. Furthermore, similar to our case, CML patients developing AML with Ph-negative and normal chromosome abnormalities have been reported. We suggest vigilant monitoring during TKI therapy and stress the importance of further analysis based on similar accumulated cases.