Gastrointestinal stromal tumors (GISTs) are potentially malignant mesenchymal tumors that can give rise to distant metastases, mainly in the liver. The co-occurrence of synchronous primary liver tumors (e.g., hepatocellular carcinoma (HCC)) in patients with GIST is extremely rare. This report describes a 77-year-old male patient with liver metastasis of GIST originating in the small intestine and synchronous HCC. The patient had undergone resection of the small intestine for the primary GIST 3 years earlier and partial hepatectomy and radiofrequency ablation for liver metastases of GIST 1 year earlier. Despite the continuation of adjuvant therapy with imatinib, two new lesions in the liver were detected by follow-up computed tomography scanning, which showed the gradual enlargement of one tumor. A second hepatectomy was performed. Pathological examination revealed that one tumor was a liver metastasis of GIST and the other was a primary HCC. To our knowledge, this is the first report of the synchronous co-occurrence of a liver metastasis of GIST and a primary HCC.