Gastrointestinal stromal tumors (GIST) are highly frequent mesenchymal tumors of the digestive tract, which mainly affect the stomach and small intestine. GISTs frequently exist with unclear symptoms. Their initial clinical presentation as acute abdomen due to their perforation is particularly rare. In the present study we report a case of a 59-year-old male presenting with acute abdomen. The final diagnosis revealed a small bowel perforation due to GIST. In this paper, we report the clinical manifestation as well as computed tomography and histopathological findings helpful for the accurate diagnosis of this rare complication of GIST. Emergency laparotomy and complete resection of tumor are essential. Following surgical resection, adjuvant tyrosine kinase inhibitor therapy should be considered for prevention of early recurrence.