A 79-year-old male was referred to the hospital with a history of abdominal discomfort. Abdominal computed tomography revealed a cystic tumor with irregular wall thickness, approximately 50 mm in diameter, along the lesser curvature of the gastric body. Magnetic resonance imaging visualized the mass as signal-hyperintense on T2-weighted imaging. Esophagogastroduodenoscopy showed a submucosal tumor with normal mucosa. Surgery was performed and the 60 × 50 × 50 mm mass was resected. The resected tumor comprised cystic and solid regions; the cystic region was filled by light bloody serous fluid. On histological examination, a solid region of the resected tumor showed a spindle-cell appearance. The diagnosis was gastric gastrointestinal stromal tumor (GIST) with predominant cystic formation. GISTs are usually solitary tumors, but in this case the tumor demonstrated extremely predominant cystic formation. Lesions with a hemorrhage or necrosis may form large cystic spaces. GISTs may show extensive cystic changes in response to tyrosine kinase inhibitor treatment; however, this patient had not undergone any such treatment before diagnosis. This represents an interesting case of a gastric GIST with predominant cystic formation occupying most of the tumor volume. Care should be taken to differentiate between GISTs and actual intra-abdominal cystic lesions.