Background: Clival chordoma is a locally aggressive tumor originating from remnants of the embryologic notochord. Although clival chordomas account for only 0.2% of all central nervous system tumors, they are characterized by local invasion and destruction, dural invasion, bone erosion, and cranial nerve palsy, and even metastasis. Case Description: We report a case of a 49-year-old female with an intradural spinal seeding metastasis 16 months after the initial endoscopic endonasal surgery (EES) for a clival chordoma. Gross total resection of tumor in upper clival region was achieved after initial EES and pathology revealed a classic chordoma. After 10 months, follow-up magnetic resonance (MR) showed a recurrence in situ and gamma knife was applied. After 16 months, the patient complained of neck pain and MR showed a new lesion in the spinal canal at C1 to C2 level. After craniotomy, the lesion in the spinal canal was totally removed, and pathology confirmed a chordoma with increased proliferative potential. The spinal chordoma might have occurred as a result of intradural spinal seeding metastasis through cerebral spinal fluid the during the initial operation. Conclusions: Chordomas are not only locally aggressive but also unpredictable and may metastasize through cerebral spinal fluid. Intensive follow-up is of great importance in the long term postoperatively time for clival chordoma patients.