Gastrointestinal stromal tumors are very rare mesenchymal tumors of the gastrointestinal tract with variable clinical presentations depending on the tumor size and anatomic site. The currently used diagnostic modalities cannot establish a preoperative diagnosis with 100% certainty. The treatment of choice includes complete surgical excision and/or chemotherapy. In this paper, we present a very rare case of gastrointestinal stromal tumor presenting with closed perforation of the small intestine. The patient was successfully managed with surgical excision of the tumor with segmental bowel resection and adjuvant chemotherapy. Although rare, it must be kept in mind that gastrointestinal stromal tumors can also present with closed bowel perforation.