Allocating patients with acute myeloid leukemia and high-risk cytogenetic abnormalities (HR-AML) for allogeneic hematopoietic stem cell transplantation (allo-HSCT) is part of the standard treatment protocol; however, whether allo-HSCT truly improves the outcomes in these patients is debatable. Data on 169 children and adolescents with HR-AML who received their first allo-HSCT in first or second remission between 2000 and 2015 were extracted from a nationwide, Japanese HSCT registry. The 3-year disease-free survival (DFS) and overall survival (OS) rates were 55.2% (95% CI, 46.8-62.9%) and 69.6% (61.4-76.3%), respectively, for all the HR-AML patients. In univariate analysis, the cytogenetic subgroup had a significant impact on both the DFS (P = 0.011) and OS (P < 0.001) rates. In particular, 14 patients with t(16;21) showed an extremely poor outcome. Additionally, older age at allo-HSCT (10-19 years old, P = 0.025), myeloablative conditioning with total-body irradiation (P = 0.019), and grade II-IV acute graft-versus-host disease (GVHD, P = 0.049) were associated with inferior OS. The donor type and occurrence of chronic GVHD did not affect the outcome. Multivariate analysis revealed t(16;21) to be associated with increased overall mortality (hazard ratio = 4.416, P < 0.001). Because the outcome of patients with certain HR-AML subgroups, such as t(16;21)-positive cases, is extremely poor even with allo-HSCT in remission, a novel therapy is urgently required.