Lymphoepithelial cysts are usually found on the lateral region of the neck. Rarely, however, lymphoepithelial cysts can be found in the oral cavity. Here, we report a case of lymphoepithelial cyst located in the floor of the mouth, in a 57-year-old man. The patient complained of a painless swelling of the floor of the mouth. During the course of the first medical examination, a circumscribed oval mass was found in the floor of the mouth just at the right side of the lingual frenum, measuring approximately 9×8mm. The clinical diagnosis was a cystic lesion. Under local anesthesia, the lesion was totally excised. Histologically, the cyst was lined with stratified squamous epithelium, and the surrounding area revealed large amounts of lymphoid tissue showing a various germinal center. The histopathological diagnosis was a lymphoepithelial cyst. There was no evidence of recurrence in the patient for 10 months after the operation.