Patients with haematological malignancies involving the NUP98 gene have been reported to have an aggressive clinical course and a poor outcome. We report successful treatment of a 15-year-old Japanese boy with acute myelomonocytic leukaemia having t(2;11)(q31;p15) and a novel fusion transcript, NUP98-HOXD11. He achieved complete remission by combined chemotherapy, and underwent unrelated cord blood transplantation 4 months after diagnosis. He is in complete remission 24 months after diagnosis. Monitoring of minimal residual disease (MRD) showed the absence of fusion transcript 12 months after transplantation. This is the first report of monitoring MRD in a patient with haematological malignancy involving NUP98 fusion transcripts.