Heterotopic pancreas, also known as ectopic pancreas, is found mainly in the stomach, duodenum, or jejunum. Pancreatic intraepithelial neoplasia (PanIN) is the non-invasive precursor of pancreatic cancer and gastritis cystica profunda (GCP) is considered a precursor of gastric cancer. As with most putative cancer precursor lesions, the diagnosis and treatment of these lesions has been controversial. A patient with no history of gastric surgery visited our institution for a regular evaluation. Endoscopy showed a 2 x 2 cm sized, protruding mass lesion with overlying normal mucosa on the fundus of stomach. Endoscopic ultrasound (EUS) and computed tomography (CT) led to the possible diagnosis of a gastrointestinal stromal tumor with cystic change. Laparoscopic gastric wedge resection was performed with intra-operative endoscopic guidance. Microscopic examination identified the mass as pancreatic tissue. Furthermore, it demonstrated PanIN, grade 3 (PanIN-3) mixed pancreatobiliary and intestinal type, arising in the heterotopic pancreas and associated with GCP. This report describes a rare case of a PanIN lesion combined with GCP as precursors of precancerous lesions in heterotopic pancreas and stomach.