We report the unique case of a 69-year-old man with an extra-gastrointestinal stromal tumor (EGIST) in the lesser omentum. Based on the location of the tumor and the radiological findings, we made a provisional diagnosis of hepatic cavernous hemangioma in the lateral segment. However, after 5 years of follow-up, tumor growth was noted and the patient underwent a laparotomy. The tumor was located in the lesser omentum and resected en bloc with its fused lesser omentum and an adherent portion of the liver. The pathology results indicated an EGIST with microscopic proliferation of epithelioid cells in the lesser omentum; the tumor was immunohistochemically negative for KIT staining and positive for CD34 and PKC theta. Because of the rarity of mitotic figures and the low Ki-67 labeling, the tumor was diagnosed as a KIT-negative EGIST with a low malignant potential. The patient was followed up without receiving imatinib mesylate treatment and has remained free of any signs of recurrence for 26 months. The present case report describes a very rare lesser omental KIT-negative EGIST.