An unusual case of an intraneural ganglion cyst of the hypoglossal nerve is presented. Only one case of this rare clinical entity has been reported previously. A 51-year-old woman presented with a 6-month history of left-sided hypoglossal nerve palsy. Magnetic resonance imaging revealed a cystic lesion related to the hypoglossal canal. There was no enhancement of the lesion after administration of Gd. A high-resolution computerized tomography scan of the skull base demonstrated an enlargement of the hypoglossal canal. To access the lesion, a far-lateral endoscope-assisted microsurgical approach was used. An intraneural ganglion lesion invading the hypoglossal nerve was found and resected. A histopathological examination confirmed that the lesion was an intraneural ganglion cyst. The occurrence of an intraneural ganglion cyst at the hypoglossal nerve is very rare. This case exemplifies an atypical location of a synovial cyst with cranial nerve involvement.