Dedifferentiated chordoma is a rare, aggressive, chemoresistant and radioresistant malignancy arising from notochord remnants that can occur anywhere along the spine. Incidence in patients under 20 years of age is 1 per 250 million. We report a case of dedifferentiated clival chordoma presenting in a 3-year-old boy with pulmonary metastasis, which responded unusually well to chemotherapy, achieving complete metastatic clearance and debulking of the primary tumour. Proton beam therapy achieved further tumour control, with excellent quality of life for multiple years. On disease relapse, an atypical lateral transcondylar surgical approach achieved complete macroscopic clearance but there was cutaneous seeding. This, and continued primary site activity, failed to be controlled with targeted therapy, traditional chemotherapy and photon radiation, resulting in gradual neurological decline and death. Intensive management resulted in above-average survival despite diagnosis late in the disease course, which may be of value directing investigation into optimal management.