Clival chordoma with occipito-cervical (OC) joint invasion can result in preoperative and postoperative instability. The authors investigate the appropriate timing of OC fusion to prevent instability-, fusion-, and surgery time-related morbidity. Twenty-two consecutive patients underwent surgery for clival chordoma from December 2008 to September 2014. OC fusion was performed for patients with OC joint invasion and instability due to preoperative destruction of the occipital condyle or extensive postoperative condylectomy. The data in relation to OC joint instability, fusion, and surgery time were analyzed retrospectively and compared between OC fusion before and after tumor resection. Of the 22 patients, 8 with tumor invasion of the OC joint underwent OC fusion. OC fusion was performed after tumor resection in one-stage for four patients and before tumor resection in two-stage for four patients. There was OC joint instability from tumor destruction of the occipital condyle in seven patients (87.5%). Patients with OC fusion after tumor resection encountered complications such as surgery site wound dehiscence, encephalitis, and cardiac arrest with consequent mortality in one patient. These complications were avoided in subsequent patients where OC fusion was performed before tumor resection. There were no differences in the extent of tumor resection between OC fusion before and after tumor resection. Two-stage OC fusion before tumor resection can reduce instability-, fusion-, and surgery time-related morbidity and achieve feasible tumor resection when OC joint instability is expected. The extent of tumor invasion and brain stem compression should be considered when fusion precedes tumor resection.