Objective To investigate the efficacy and the clinical follow-up of hematopoietic stem cell transplantation (HSCT) for systemic mastocytosis associated with acute myeloid leukemia (SM-AML) in children. Methods The clinical data and follow-up results of 2 children with SM-AML treated by HSCT were retrospectively analyzed, and the related literature was reviewed. Results There were 2 children (1 boy and 1 girl) with SM-AML, aged from 2 to 9 years. The onset symptom of 2 cases was fever with abnormal blood image, and bone marrow smear cytology showed increased myeloblasts and spindle or atypical mastocytosis. The karyotype of t(8;21)(q22;q22) and AML1-ETO fusion gene was positive. The variation of KIT V560D (exon 11) was found in one child, and the variation of KIT T418_D419del (exon 8), KIT N822K (exon 17), and NRAS G13D (exon 2) were found in another child. After diagnosis of SM-AML, induction chemotherapy and consolidation chemotherapy were given according to CCLG-AML 2019 regimen. Bone marrow smear morphology after chemotherapy showed complete remission of AML and increased mast cells (6.6%-27.6%). One patient was treated with HSCT from HLA-mismatched unrelated umbilical cord blood donor (9/10), and the pretreatment regimen was fludarabine + busulfan (Bu) + cyclophosphamide (CTX). One patient was treated with HSCT from HLA-mismatched sibling donor (9/10, elder sister donor), and the pretreatment regimen was cytarabine + Bu + CTX+ fotemustine + antithymocyte globulin. The number of returned nuclear cells was 7.69×10⁸/kg and the number of returned CD34⁺ cells was 1.31×10⁵/kg in one patient. The number of mononuclear cells was 9.08×10⁸/kg and the number of returned CD34⁺ cells was 6.81×10⁶/kg in another patient. Hematopoietic function was reconstructed in 2 children with SM-AML. The time of neutrophils engraftment and platelet engraftment after transplantation were 11-27 d and 13-47 d, respectively. Two patients were followed up until August 2022, and they both survived. Mast cells and AML1-ETO fusion gene turned negative in one patient. Mast cells persisted in another patient, and the AML1-ETO fusion gene was still positive. Conclusions HSCT is feasible for the treatment of SM-AML. The regimen of chemotherapy before transplantation and the key problems of transplantation are worthy of further study.