Background Intramural esophageal bronchogenic cyst is very rare. Surgical removal of the cysts is advised even the patients are asymptomatic, since the cyst can lead to complications, and there is a risk of malignant transformation. Thoracotomy or thoracoscopy is the most commonly used approach for complete excision of the cysts. To our knowledge, this is the first report to excise intramural esophageal bronchogenic cyst completely by endoscopic submucosal tunnel dissection (ESTD). Case presentation A 40-year-old male was referred to our hospital due to the detection of a submucosal tumor at the distal esophagus. The tumor was found during gastroendoscopy in a general health check-up. The patient had no symptoms. A benign esophageal tumor was confirmed by endoscopic ultrasonography (EUS) and computed tomography (CT). On the basis of these results, ESTD was performed. During the procedure, a cystic mass was observed between the mucosa and the muscular layers of the esophagus, and a hybrid knife was used for dissection. Histopathological examination showed the cyst wall was lined by pseudostratified ciliated columnar epithelium, consistent with a bronchogenic cyst. The esophagography using meglumine diatrizoate showed no leakage on the seventh day after ESTD. The patient remained asymptomatic and had a regular diet during the follow-up period. Discussion and conclusions We successfully utilized ESTD for complete removal of esophageal bronchogenic cysts originating from the muscularis propria. The approach appeared safe, providing a minimally invasive treatment option for patients.