Abstract A 54‐year‐old man was referred to our hospital because of a suspected esophageal submucosal tumor on upper gastrointestinal radiography. Contrast‐enhanced computed tomography showed a 52 mm homogeneous mass attached to the lower thoracic esophagus. Esophagogastroduodenoscopy revealed a 50 mm submucosal tumor in the lower esophagus, and endoscopic ultrasonography (EUS) showed a continuous hypoechoic lesion in the esophageal muscularis propria. Contrast‐enhanced harmonic EUS revealed a non‐echogenic area. T1 and T2 magnetic resonance imaging revealed a high‐signal lesion. Based on imaging studies, an esophageal duplication cyst was diagnosed. Although asymptomatic, the patient underwent video‐assisted thoracic surgery because of the possibility of rupture and the appearance of symptoms due to a future infection or enlargement, although this was not noted before. In our case, the esophageal duplication cyst appeared as a hypoechoic mass, requiring differentiation from submucosal tumor other than the cyst. Histologically, the cyst was covered by two layers of muscle covered by the chorioepithelial columnar epithelium. EUS fine‐needle aspiration is effective in diagnosing submucosal tumor but also carries the risk of infection. Contrast‐enhanced ultrasonography was used in this case to observe the interior and reach a preoperative diagnosis. Contrast‐enhanced harmonic EUS appears to be effective in examining the interior of submucosal tumor lesions noninvasively.