We report herein a rare case of malignant transformation of aberrant pancreas in the stomach, associated with gastric outlet obstruction. A 58-year-old woman was admitted to our hospital, complaining of vomiting. Although barium meal examination and gastric endoscopy showed marked pyloric stenosis, the biopsy specimen obtained from the stenotic site revealed regenerative mucosa without malignancy. Abdominal computed tomography and endoscopic ultrasonography (EUS) also could not detect the cause of the obstruction. Histopathological examination of the surgically resected specimen showed the malignant transformation of aberrant pancreas in the stomach. It should be noted that one of the causes of gastric outlet obstruction may be aberrant pancreas or its malignant transformation.