According to the 2016 World Health Organization classification, a germline DEAD‐box helicase 41 gene (DDX41) mutation with myeloid neoplasms has been newly classified. The clinical course of acute myeloid leukemia (AML) with a germline DDX41 mutation has not yet been clarified. In the early phase, this condition is slowly progressive, the rate of remission induction is high, and the prognosis is good. On the other hand, in the late phase, the gradual relapse rate increases and the ultimate prognosis can be poor. Currently, clear guidance on the indication for allogeneic hematopoietic stem cell transplantation (allogeneic HSCT) for AML with a germline DDX41 mutation has not been yet provided. However, we consider that allogeneic HSCT should be performed in patients who are eligible for allogeneic HSCT for germline DDX41 mutations in AML to overcome poor relapse‐free survival, referring to previous relevant papers. We report a 49‐year‐old patient who had pancytopenia and was finally diagnosed with a germline DDX41 mutation and AML. We decided to perform allogeneic HSCT. On day 68, he was complicated by acute graft versus host disease, gut stage 1, grade II, and was started on prednisolone 0.2 mg/kg. He recovered quickly and has been currently alive without symptoms of graft versus host disease for almost 2 years. Regarding donor search for allogeneic HSCT for AML with a germline DDX41 mutation, it is essential to ensure that the donor must be negative for this mutation when the donor is a family donor. If the related donor has a positive mutation, which can cause the development of donor‐derived leukemia, allogeneic HSCT should performed from an unrelated donor.