Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms of the gastrointestinal tract. Although most patients with advanced GISTs benefit from imatinib mesylate (IM) as standard targeted therapy, the optimal duration of adjuvant IM for GIST patients with high risk of recurrence who underwent surgical resection remains unknown. In this article, we present a case of a ruptured GIST of the small intestine accompanied by peritoneal metastases, which was effectively treated by surgical procedure followed by long-term adjuvant therapy with IM. Surgical resection was performed for the ruptured small intestinal GIST, and multitude of peritoneal metastases were cauterized. The patient received adjuvant therapy with IM (400 mg/day) for 12 years without an interruption or a dose change. Peritoneal metastatic recurrence was observed by the follow-up computed tomography scan obtained 12 years after surgery, and surgical resection of the recurrent GIST was performed. The molecular examination indicated a KIT exon 11 deletion mutation in both the primary GIST and recurrent GIST. An additional point mutation was observed in the recurrent GIST in exon 17 that caused resistance to IM. The present case might indicate that extensive removal of the tumor cells through surgery and long-term administration of IM without an interruption or a dose change were important for achieving improved recurrence-free survival in patients with ruptured GISTs of the small intestine with peritoneal metastases.