Clival chordoma is a rare malignant tumor of the brain that typically occurs in older adults. It has a high local recurrence rate and is hence associated with poor prognosis. Here, we report a case of an adolescent who presented with a 1-month history of worsening headache and blurring of vision, as well as a 6-month history of left-sided facial and body numbness. Clinical findings were consistent with left upper motor neuron lesion of the seventh cranial nerve with involvement of the fifth cranial nerve. He was also found to have a sixth cranial nerve palsy demonstrated by diplopia upon lateral gaze with no evidence of papilledema. Magnetic resonance imaging of the brain suggested clival chordoma. He was subsequently referred to the neurosurgical team, and he successfully underwent an endoscopic trans-sphenoidal surgery to excise the lesion. He recovered well, continued his follow-ups with the neurosurgical team, and showed good progress. He also attended regular follow-ups with his primary care physician to ensure ongoing psychosocial support and monitoring of his overall health status. This case demonstrates the importance of prompt identification and treatment of clival chordoma in an adolescent. Long-term follow-ups and shared care between primary and secondary care physicians are essential to monitor recurrence of tumor and to provide psychosocial support.