The aim of the study was to analyze clinical features of lymphoepithelial cyst (LEC) to make a more comprehensive and deeper understanding of it. We retrospectively analyzed the hospital records of 201 patients who were diagnosed by pathology results. Clinical characteristics like demographic profiles, lesion characteristics, therapeutic schedule, and associated costs were analyzed. Patient’s age ranged from 17 to 83 years old (52.6 ± 14.3, 120 males and 81 females). There were 12 cases of pancreatic LEC, 48 of oral LEC, and 141 of parotid LEC. Single lesion was found to be more than multiple lesions (147:54, 73.1%:26.9%). The majority of patients was primarily diagnosed by imaging test and endoscopy (171, 85.1%). All patients were finally confirmed by pathology results. Different treatment plans were selected according to personal situation, including dynamic observation (21, 10.5%), non-surgical treatment (24, 11.9%), and surgical treatment (156, 77.6%). No recurrence was found in surgical treatment patients for up to 24 months follow-up. To sum up, LEC is a rare and benign lesion, which is mostly located at parotid and oral, rarely located at pancreas. No typical symptoms could be found. EUS-FNA could be a reliable way to obtain pathological diagnosis. LEC could be cured by surgical resection with no recurrence.