Xanthogranulomatous gastritis (XGG) is a rare inflammatory lesion of the stomach, with only 11 reported cases worldwide. Furthermore, reports on the use of detailed diagnostic imaging in XGG are not available. Herein, we describe a case of XGG with detailed diagnostic imaging mimicking malignant gastrointestinal stromal tumor (GIST) in light of the current literature. A 79-year-old woman who presented with epigastric pain was referred to our hospital. Upper gastrointestinal endoscopy revealed an elevated lesion similar to a submucosal tumor (SMT). F-18 fluorodeoxyglucose positron emission tomography/computed tomography (FDG PET/CT) showed intense FDG uptake in the mass. Additional imaging studies revealed a malignant GIST, which was suspected of having infiltrated the left lobe of the liver. Open surgery was carried out, but tumorous lesions were not found. For exact histopathological diagnosis, partial resection of the thickening gastric wall was performed, and XGG was diagnosed. We conclude that benign conditions, including XGG, should be considered when intense FDG uptake in SMT is found.