We report a case of a 50-day old infant presenting to us post excision of a nasopharyngeal mass leading to respiratory distress at birth. Initial imaging had shown a clival mass and neuroimaging showed findings suggestive of Tuberous Sclerosis. Histopathology of the excised mass was suggestive of a chordoma. A rare association between Tuberous Sclerosis and pediatric chordomas is known to exist and is exemplified by this case report. We have also discussed the various challenges encountered during the management of such patients due to the location of these tumors and difficulty in using radiotherapy at a very young age.