The occurrence of adenopathy in patients with myelodysplastic syndrome-associated extramedullary myeloid cell tumors has rarely been reported. We describe a 7-year-old girl with juvenile myelomonocytic leukemia who showed the novel chromosomal abnormality t(9;12)(p22;q24.1) and who developed severe adenopathy of the cervical lymph nodes, tonsils, and adenoids that was manifested as granulocytic sarcoma. Following chemotherapy, the patient underwent a conditioning regimen of busulfan, cyclophosphamide, and total body irradiation followed by successful allogeneic bone marrow transplantation from her single HLA locus-mismatched mother at 6 months after her diagnosis. The patient continues to be well and in remission 3 years after stem cell transplantation.