A 68-year-old woman with essential thrombocythemia had been treated with hydroxycarbamide and aspirin for 13 years. She exhibited the rapid progression of anemia, and a bone marrow examination showed dysplasia of the erythroid cells, myeloid cells, and megakaryocytes. Karyotype analysis indicated complex abnormalities including der (5;21)(p10;q10). She was diagnosed with myelodysplastic syndrome (MDS), refractory anemia with excess blasts-1 (RAEB-1). Lenalidomide was started, but no improvement in anemia was recorded. Lenalidomide was discontinued due to eosinophilia, basophilia, and a skin rash. Azacitidine was administered. The patient became transfusion independent, and a complete cytogenetic response was achieved with three courses of azacitidine. However, disease progression to acute myeloid leukemia (AML) was observed after an additional two courses of azacitidine, which was resistant to induction chemotherapy. The patient died five months later from AML transformation. Azacitidine may be effective in MDS transformed from essential thrombocythemia, and also in lenalidomide-resistant MDS with the deletion of 5q.