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An 80-year-old man was diagnosed with acute myeloid leukemia (AML), and molecular analysis identified FLT3-ITD, TKD mutations. Induction chemotherapy with daunorubicin plus cytarabine achieved hematological complete remission; however, extramedullary infiltration was detected in the skin and central nervous system. Due to this extramedullary disease, treatment with mitoxantrone plus high-dose cytarabine was administered, leading to systemic complete remission. Two cycles of the same regimen were then added. The patient relapsed 5 months later, at which time FLT3 mutations were no longer detectable by a companion diagnostic test. However, targeted sequencing analysis identified a novel FLT3-ITD positive minor clone. Treatment with venetoclax plus azacitidine was then started. The patient achieved complete remission and has remained relapse-free for more than 2 years. In this case, the FLT3 mutation companion diagnostic test result became spontaneously negative without FLT3-directed treatment, and the response to venetoclax plus azacitidine was favorable. This case highlights the importance of molecular testing not only at diagnosis but also at relapse for appropriate treatment selection.