We report a case of an intraneural ganglion cyst of the hypoglossal canal. The patient presented with unilateral hypoglossal nerve palsy, and magnetic resonance imaging showed a small lesion in the hypoglossal canal with no contrast enhancement and high signal on T2-weighted imaging. The lesion was assumed to be a cystic schwannoma of the hypoglossal nerve. Stereotactic irradiation was considered, but in accordance with the patient's wishes, surgical exploration was performed. This revealed that, rather than a schwannoma, the patient had an intraneural ganglion cyst, retrospectively contraindicating irradiation as an option. This case illustrates a very rare location of an intraneural ganglion cyst in the hypoglossal nerve. To our knowledge there are no previous reports of an intraneural ganglion cyst confined to the hypoglossal canal.