A 65-year-old man presented with abdominal bloating for approximately 4 weeks. After CT imaging, it was diagnosed as gastric carcinoma with hepatic metastasis. 68Ga-FAPI-04 PET/CT revealed much higher tumor-to-background contrast and more metastatic lesions compared with 18F-FDG PET/CT in this case. Following gastroscopy and pathological examination, the final diagnosis was malignant gastrointestinal stromal tumor. This case demonstrated that 68Ga-FAPI-04 PET/CT was more sensitive than 18F-FDG PET/CT for detecting primary and metastatic lesions in malignant gastrointestinal stromal tumor.