We report the first documented case of pancreatic metastasis from a gastrointestinal stromal tumor of the stomach. A 42-year-old Japanese man presented with severe abdominal discomfort. Computed tomography of the abdomen showed a huge heterogeneous mass consisting of cystic and solid components in the left upper abdomen. F-18-Fluorodeoxyglucose positron-emission tomography revealed high tracer uptake in the abdominal mass. After total gastrectomy with lymphnodectomy was performed, a hard mass was palpated in the pancreatic tail. The pancreatic tumor was also resected under the therapeutic strategy. Histological examinations of the resected gastric and pancreatic specimens revealed that both tumors consisted of uniform spindle cells with a fascicular growth pattern and were immunohistochemically positive for CD34 and CD117/KIT. Gene sequencing analysis of DNA from each tumor revealed an identical deletion of 21 nucleotides in exon 11 of the gene KIT. On the basis of these results, we concluded that the pancreatic tumor was a metastatic tumor from the gastrointestinal stromal tumor of the stomach.