We describe a case with rapid relapse after resection of a sunitinib-resistant gastrointestinal stromal tumor (GIST). Liver metastases and foci of left retroperitoneal recurrence developed during adjuvant imatinib treatment. The tumors did not shrink after sunitinib treatment, and hepatectomy and retroperitoneal tumorectomy were performed. Histological examination showed a Ki67 labeling index of over 50% in viable tumor cells. Genomic analysis revealed mutations in exons 11 and 13 of the c-KIT gene. Computed-tomographic scan revealed retroperitoneal recurrence at the surgical site five weeks post-operatively. In this case, high proliferative activity of the recurrent foci was associated with resistance to sunitinib and rapid recurrence during the perioperative withdrawal of sunitinib. It is important to consider the possibility of an exon 13 mutation with an aggressive phenotype when treating sunitinib-resistant GISTs. Surgical intervention for sunitinib-resistant GISTs should be carefully considered if R0 resection is not possible.