Objective To investigate the feasibility and effectiveness of sequential decitabine after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in the treatment of children with Fanconi anemia (FA) progressing to acute myeloid leukemia (AML). Methods The clinical data of an 8-year-old girl with progression from FA to AML who received haploid transplantation (younger brother as donor) followed by decitabine maintenance therapy were retrospectively analyzed. Results The child presented with anemia at 6 years old and Fanconi anemia was diagnosed at 8 years old. The child was treated with cyclosporine and testosterone undecanoate for 6 years without response, presenting with progressive trilineage decline and ineffective platelet transfusions, and finally was diagnosed with AML by bone marrow examination. The results of bone marrow NGS test showed c.3348+1G>A homozygous variation in FANCA gene. The patient was treated with FLAG (fludarabine+cytarabine+granulocyte colony-stimulating factor) chemotherapy followed by a myeloablative preconditioning regimen based on whole body irradiation. Granulocyte and platelet were engrafted 15 days after transplantation. After transplantation, the child was given a reduced dose of cyclosporine and she maintained grade Ⅱ skin graft-versus-host disease until 1 year after transplantation. From 6 months after transplantation, decitabine was administered every 2 months for a total of 6 times, and the expression level of WT1 was monitored. It has now been nearly 6 years since the transplantation, and the child is in event-free survival. Conclusions The allo-HSCT combined with decitabine sequential therapy is effective in the treatment of AML progression from FA.