Allogeneic hematopoietic stem cell transplantation (HSCT) can be used to treat children with refractory acute myeloid leukemia (AML). This retrospective analysis aimed to describe the outcomes and risk factors in such children. Data were collected through the nation-wide registry program in Japan. A total of 417 AML (median age: 13 years) patients 20 years or younger at HSCT, between January 2001 and December 2015, were included. A total of 314 patients died, and the median follow-up duration of the survivors was 1052 days. The most frequent cause of death was leukemia progression (58%). The 3-year overall survival (OS) rate was 23% (95% confidence interval [CI]: 19-28%). Chronic GVHD was associated with improved 3-year OS (47%, 95% CI, 36-57%, hazard ratio: 0.603, p = 0.001). Low performance status, presence of more than 25% of marrow blasts, presence of blasts in the blood at transplantation, FAB (other than M1 or M2), male donors, and number of transplantations ≥ 2 were adverse pre-HSCT variables. Patients with 0, 1-2, 3-4, 5, and 6-7 pre-HSCT variables had 3-year OS rates of 52%, 32%, 19%, 8, and 0%, respectively. Our findings may help experts decide if HSCT should be performed in such cases.