Gastrointestinal stromal tumors (GIST) are relatively rare and often present with vague symptoms. Their first clinical manifestation as acute abdomen due to perforation is extremely rare. We report a rare case of spontaneous perforation of exophytic gastrointestinal stromal tumor (GIST) causing perforation of jejunum. A 61 year, male patient presented with symptoms of acute abdomen. After evaluation, a laparotomy was performed, where perforation of a tumor in the jejunum was found. The perforated part along with the tumor was resected and the histopathological examination showed that the tumor was GIST. In emergency setting the patients with perforation peritonitis, a diagnosis of spontaneous perforation of GIST though rare should be kept in mind specially in elderly patients.