Chordomas are the tumors commonly involving base of skull which are predominantly solid in consistency. A cystic chordoma of the cavernous sinus is an extremely rare entity and has never been reported. We report a 26-year-old male presenting with gradually progressive right-sided sixth nerve palsy and headache. Computed tomography and magnetic resonance imaging of the brain showed a cystic lesion in the right cavernous sinus. The patient was successfully treated using a transnasal endoscopic transsphenoidal approach. Histopathological examination of the lesion revealed chordoma. Our case is the first report of such a condition. Chordoma should be considered in the differential diagnosis of cystic lesions in the parasellar location. We briefly review the radiology, the pathology and management dilemmas of such lesions.