Abstract Background A 32-year-old man diagnosed with acute myelomonocytic leukemia (M4) concurrently had active Crohn's disease (CD) that was refractory to azathioprine and anti-tumor necrosis factor. Case Report He underwent an allogeneic bone marrow transplantation from a one HLA-DR allele-mismatched unrelated donor to achieve the first complete remission of leukemia. The conditioning regimen consisted of fludarabine (180 mg/m2) and busulfan (8.0 mg/kg) without T-cell depletion. Graft-versus-host disease (GVHD) prophylaxis included tacrolimus and mycophenolate mofetil. Cefotaxime was prescribed for a secondary bacterial infection in a perianal abscess before the start of conditioning chemotherapy. Although low-grade diarrhea persisted, there were no signs of either acute GVHD or CD in the mucosal biopsy specimens on day 24. Complete remission of leukemia and near remission of CD were sustained for 20 months after transplantation without any immunosuppressive drug. Conclusions Allogeneic heamtopoietic stem cell transplantation with reduced-intensity conditioning is a possible therapeutic option for patients with severe and/or refractory CD.