BackgroundThe oral lymphoepithelial cyst (LEC) is a rare, soft-tissue, developmental cyst, initially presented by Gold in 1962 as a “branchial cleft cyst”. It may occur in the pancreas, tongue, neck, and other regions of the oral cavity. No study has been reported in Pakistan and Karachi reporting a case of lymphoepithelial cyst in the submandibular region. This rare case of LEC has been reported to help the clinicians to bring LEC into their differential diagnosis for lesions affecting the submandibular region.Case presentationWe report a case of 57 years old female reported to the Maxillofacial OPD of a tertiary care hospital with the complaint of swelling on the right side of the neck for 3 weeks which was rapidly increasing in size. She was having difficulty in mastication. On extra-oral examination, there was swelling on the right side in the submandibular area. The overlying skin is normal with no evidence of pus and discharge. On palpation, the swelling was soft, non-tender, non-fluctuant, non-displaceable into the submandibular area. Lymph nodes were impalpable. Excision of the lesion performed under general anesthesia and biopsy revealed lymphoepithelial cyst associated with submandibular gland. Here we present an attention-grabbing case of swelling in the right submandibular region which was provisionally diagnosed as a malignant submandibular lymph node however later evidence histopathologically as a lymphoepithelial cyst of the submandibular gland.ConclusionAn unusual cause of swelling in the neck is lymphoepithelial cysts. Submandibular gland appearance is not usual and can prove to be a clinical problem.