Gastrointestinal stromal tumors (GISTs) are rare malignant tumors and only a few reported cases of brain metastases can be found. Introduction of a new molecular targeted agent, imatinib mesylate in the last decade has dramatically changed the treatment strategy and prognosis. However, imatinib is usually ineffective for brain metastasis from GISTs. The authors present the case of multiple brain metastases from jejunal GIST. The brain metastasis in the right prefrontal gyrus was detected 20 months after resection of the primary lesion when left hemiparesis began although the patient was on imatinib. Then the patient began taking sunitinib instead of imatinib, and the lesion shrunk and the symptom improved. However, after the dose reduction due to side effects, a new brain metastasis was found and this time, stereotactic radiation was effectively done. Sunitinib is one of the promising receptor tyrosine kinase inhibitors used for metastatic renal cell carcinomas or imatinib-refractory GISTs. Sunitinib is thought to penetrate blood-brain barrier, and recent reports indicate effectiveness to brain metastasis. To the authors' knowledge, this is the first report of brain metastases from jejunal GIST responding to sunitinib therapy.