Rationale: Isolated myeloid sarcoma (MS) is characterized by the rapid proliferation of myeloblasts of acute myeloid leukemia (AML), without any blood or bone marrow involvement. This disease can manifest with extramedullary organ involvement, such as the skin, lymph nodes, bone, brain, breast cervix, and visceral organs, while the occurrence of myeloid sarcomas in the stomach is rare. Isolated MS has been associated with acute myeloid leukemia (AML), but the rapid progression of MS to acute myeloid leukemia with a complex karyotype and TLS-ERG fusion gene is even rarer.Patient concerns: A 33-year-old woman suffered from persistent epigastric pain accompanied by two months of anorexia and nausea, as well as 1-week of melena.Diagnosis: This patient was initially diagnosed with gastric MS that eventually transformed into AML with a complex karyotype and TLS-ERG fusion gene, 4 months later.Interventions: Only palliative care, including nutrition support, antacids, blood transfusion, anti-infection methods were used on this patient to determine the cachexia status and the family's requirement.Outcomes: Routine follow-up results demonstrated this patient had died due to cerebral hemorrhage five months after the diagnosis of MS.Lessons: Comprehensive integration of patient history, imaging features, mass and bone marrow biopsy, and molecular cytogenetic may provide insights that could help us avoid the misdiagnosis of gastric MS. Isolated gastric MS can rapidly progress to AML with a poor prognosis if the patient does not receive appropriate treatment.