A 72-year-old woman visited our hospital for a routine health examination and underwent abdominal ultrasonography, which revealed an intra-abdominal tumor. Abdominal computed tomography and magnetic resonance imaging showed a well-defined solid mass of ~3 cm in diameter lying adjacent to the stomach. The mass was preoperatively diagnosed as gastrointestinal stromal tumor of the stomach. At laparotomy, a well-encapsulated tumor was found in the lesser omentum. It was slightly adherent to the stomach wall but was removed without difficulty. Therefore, only enucleation of the tumor was performed. The excised tumor, which was 35 × 30 × 25 mm3 in size, had a white cut surface without necrosis or hemorrhage. According to the pathological findings, the tumor was classified as a very low-risk gastrointestinal stromal tumor originating in the lesser omentum. Gastrointestinal stromal tumor of the lesser omentum is very rare, and surgical resection is the only effective treatment modality.