This 69-year-old man underwent a partial jejunectomy for gastrointestinal stromal tumor(GIST) at the age of 60, and subsequently hepatectomy of segment 5, 6, 7 for liver metastasis of GIST a year later. An irregular mass close to the cutting stump of the liver, and a mass that showed enhanced-effect at segment 4 was discovered 28 months after hepatectomy. In order to treat this second recurrence, we administered imatinib and sunitinib sequentially. The tumor subsequently became drug-resistant, so we removed it surgically together with the liver and a portion of right diaphragm, and a tumor in segment 4. The patient shows no recurrent sign 4 months after surgery. This case suggests that surgical resection should be considered for partially drug resistant GIST.