Background: a rare case of a cystic thymopharyngeal duct presented as a rare case of the cervical thymus. The embryology of normal cervical descent of the thymus is reviewed. The preoperative diagnosis of thymopharyngeal duct cyst is rare to be established, however, histopathology is the definitive diagnosis. Thymopharyngeal duct cysts are rare lesions commonly been one of differential diagnosis in childhood neck masses. Patients and Methods: asymptomatic thymopharyngeal duct cyst in a 7 years old boy caused by the remnants of the thymopharyngeal duct. A consent form was taken from the parent. The study approved by the ethical Committee of the Faculty of Medicine, UmmAl-QuraUniversity that follows the international rules of research. The study not sponsored by any agency. Results: the patient undergoes surgery under general anesthesia followed by transverse incision, the cystic lesion was found on the sternocleidomastoid muscle. There were no postoperative complications. Histopathologic evaluation confirms the presence of thymopharyngeal duct cysts. Conclusion: thymopharyngeal duct cysts can cause a diagnostic challenge to the surgeon evaluating of neck swelling. Also its importance of considering thymopharyngeal duct cysts in the differential diagnosis of any child who presents with a neck swelling.