We had a rare case of 50-year-old woman with a unilateral hypoglossus nerve palsy as a sign of clival chordoma. A computed tomography (CT) scan of the skull base showed bone destruction at the anterior part of the foramen magnum and CT scan of the neck reveals asymmetrical area at the base of the tongue. Magnetic resonance imaging showed a mass at the skull base in the region of the clivus with bone destruction in the middle and right side of the clivus. The tumor was biopsied through transnasal biopsy from the region of the clivus using a navigation system and microscopical surgical technique. Postoperatively, the patient received radiotherapy. Surgery is the most effective treatment of chordomas. An endoscopic approach provides easy, rapid and direct access to the clivus. A postoperative radiation therapy is recommended. A carbon ion radiotherapy is an effective treatment for chordomas of the skull base with minimal side effects. Close interdisciplinary collaboration between ORL, neuroradiology, pathology and oncology is desirable for effective therapy.