Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor and has a malignant potential. The clinical presentation with pneumoperitoneum and peritonitis is extremely rare. We report a case of a 40-year-old male presented with symptoms of acute abdomen. Radiological work-up confirmed pneumoperitoneum. Emergency laparatomy and complete resection were performed. The final diagnosis revealed perforated GIST originating from the jejunum. If an abdominal mass presents with pneumoperitoneum and peritonitis, jejunal GIST should be considered in diagnosis. A complete radical resection followed by postoperative adjuvant chemotheraphy with Imatinib is recommended.