Primary malignant tumors of the small intestine are rare. Malignant gastrointestinal stromal tumors are the third most common neoplasm among primary malignant small bowel tumors. A 56-year-old woman was admitted to our hospital because of appetite loss and dyspnea with movement. On admission, physical examination revealed severe anemia in her conjunctiva and a tumor in her left abdomen. Her hemoglobin level was 6.2 g/dL and other laboratory data were normal. Abdominal ultrasonograms and computed tomograms revealed a 55 x 70-mm heterogeneous mass and multiple low-density masses in the liver. Superior mesenteric arteriograms revealed a hypervascular tumor fed by the jejunal arteries. A malignant gastrointestinal stromal tumor arising from the jejunum with liver metastases was suspected. Partial resection of the affected jejunum and left trisegmentectomy of the liver were performed. The resected primary tumor was 120 x 45 x 65 mm. The tumor was mainly submucosal, but extended outside the jejunum; it was elastically firm and multiloculated. A small ulcer was seen on the mucosal side. The metastatic liver tumors were solid or cystic with diameters of 20 to 40 mm. Histopathological examination revealed that the tumors were characterized by fascicular proliferation of spindle-shaped cells. Immunohistochemical staining was positive for CD34 and c-kit, and negative for S-100 protein and smooth muscle actin. This case was a malignant gastrointestinal stromal tumor originating in the jejunum with liver metastases. The primary tumor and liver metastases were successfully resected simultaneously.