We report herein what to our knowledge is the first documented case of a malignant granular cell tumor of the stomach. A 64-year-old woman was admitted to our hospital for investigation of gastric submucosal tumor. Endoscopy disclosed a large hemispherical mass located on the lesser curvature at the gastric antrum with a normal mucosal surface, and computed tomography (CT) revealed a solid tumor about 7 cm in diameter with clear margins. A laparotomy was carried out under the preoperative diagnosis of leiomyosarcoma of the stomach. A tumor was found in the gastric antrum, with extragastric extension to the hepatic hilum, and a distal partial gastrectomy was performed. However, a follow-up CT scan performed 21 months postoperatively revealed a solid tumor of about 10 cm in diameter with clear margins, situated between the liver and the transverse colon. This was subsequently diagnosed as local recurrence and a resection was carried out. Microscopic examination of both the first and second specimens showed that the tumor cells were large and polygonal, with medullary proliferation and finely granular eosinophilic cytoplasm. Mitotic figures were also present. Thus, the lesion was diagnosed as a malignant granular cell tumor of the stomach from the clinical and pathological findings.