Gastrointestinal stromal tumors are the most common mesenchymal tumors of gastrointestinal tract which comprise <1% of all primary gastrointestinal malignancies. These tumors show mutations in the KIT gene or platelet-derived growth factor receptor-A gene and usually stains positively for CD117. Very few cases of extragastrointestinal GIST (EGIST) have been reported in literature which originate from omentum and mesentery as per our knowledge. Here, we report a case of EGIST arising from omentum with no connection to gastrointestinal tract organs in a 60-year-old woman who presented with abdominal pain for 2–3 months. Intraoperative findings showed the presence of multiple globular masses and nodules in the peritoneal cavity. Microscopically, the spindled tumor cells were arranged in interlacing fashion. Immunohistochemistry showed positivity for CD117 and negativity for smooth muscle actin (SMA). Thus, EGIST should always be considered as a differential diagnosis for nodular mesenteric masses.