Chronic myelogenous leukemia (CML) is a myeloproliferative disorder characterized by the presence of the Philadelphia chromosome. Although the major BCR/ABL transcript is present in majority of CML patients, the minor BCR/ABL transcript is rarely reported as an additional chromosomal abnormality related to the progression of CML. We describe the case of a 37-year-old woman who had CML and pain in the extremities. She was diagnosed with lymphoid blast crisis of CML on the basis of the following findings: presence of promyelocytes, myelocytes, and metamyelocytes in peripheral blood smear; detection of major and minor BCR/ABL transcripts by polymerase chain reaction analysis; proliferation of lymphoblastic cells with abnormal B-cell phenotype; and aberrant expression of myeloid antigens in the bone marrow. The patient underwent one course of idarubicin and cytosine arabinose therapy combined with imatinib followed by daunorubicin/cyclophosphamide plus vincristine and prednisone/L: -asparaginase (DNR/COP/L: -ASP) therapy, high-dose cytosine arabinose, and CHOP therapy (cyclophosphamide, doxorubicin, vincristine, and prednisolone). Subsequently, the patient underwent high-dose chemotherapy (total body irradiation and cyclophosphamide) followed by allogeneic bone marrow stem cell transplantation from a human leukocyte antigen (HLA)-matched unrelated donor. After these treatments, the patient was disease-free for 19 months. Our case suggests that these treatments may be feasible, safe, and effective for the treatment of patients with blast crisis CML expressing the minor BCR/ABL transcript.