Esophageal bronchogenic cysts are rare bronchopulmonary foregut malformations, and those located in the abdominal cavity are particularly rare. Esophageal cysts are typically found incidentally; an exact preoperative diagnosis of bronchogenic cyst is difficult, and surgical resection is generally recommended. Here, we report a case in which a subdiaphragmatic bronchogenic cyst of the esophagus coexisted with advanced gastric cancer. A 44-year-old man was referred for the treatment of gastric cancer. A preoperative examination revealed a mass on the right side of the esophagogastric junction that was preoperatively diagnosed as a metastatic lymph node. Intraoperative exploration revealed that the mass had protruded from the abdominal esophageal wall, and was diagnosed as a cyst originating from the subdiaphragmatic esophagus. The cyst was completely resected with the whole stomach and abdominal esophagus. The histopathological findings of the cyst were specific for a bronchogenic origin. The patient has not shown any signs of disease recurrence.