Gastritis cystica profunda (GCP) is a lesion characterized by elongation of the gastric foveolae with hyperplasia and cystic dilatation of the gastric glands that extends into the submucosal layer. In most cases, gastritis cystica profunda develops in patients who have undergone a gastroenterostomy, with or without gastric resection. GCP may present not only as a submucosal tumor or as solitary or diffuse polyps, but GCP is also rarely seen as a giant gastric mucosal fold. A patient arrived at our hospital with dyspepsia. Gastroduodenoscopy (EGD) showed the presence of a submucosal tumor measuring 3 cm in the widest diameter in the body of the stomach. A CT scan demonstrated the cystic nature of the lesion and endoscopic ultrasound (EUS) depicted a homogeneous hypoechoic, unilocular cystic mass without any internal solid component. EGD, CT and EUS findings suggested that the lesion was more likely to be benign than malignant. The lesion was treated with an endoscopic mucosal resection (EMR), and the lesion was finally diagnosed as gastritis cystica profunda. A follow-up EGD demonstrated that all mucosal surfaces were well healed four weeks after the EMR.