Yasutaka Hayashi and Masashi Mizumoto contributed equally to this article.Objective: To evaluate the hyperfractionated high-dose proton beam therapy (PBT) for patients with clival chordomas. Methods: Records for 19 patients with pathologically verified clival chordomas treated with surgery followed by hyperfractionated PBT were retrospectively reviewed. The first 9 consecutive patients were treated with 77.44 cobalt gray equivalents (CGEs) in 64 fractions, and the latter 10 patients were treated with 78.4 CGE in 56 fractions. Results: The median follow-up period of all 19 cases was 61.7 months with a range from 31.5 to 115.4 months. At 5 years, the local control, cause-specific and overall survival rates for all 19 cases were 75%, 94% and 83.2%, respectively. Whereas the 5-year local control, cause-specific and over all survival rates of the latter 10 cases were 100%, 100% and 88.9%, respectively, with a median follow-up period of 59.5 months. One of the first nine patients demonstrated bilateral temporal lobe radiation necrosis, who were successfully treated conservatively. In the latter cohort, two cases showed transient neurological symptoms probably due to brain stem ischaemia, but both cases recovered completely with conservative treatment. Conclusion: The hyperfractionated high-dose scheme combined with maximum surgical removal was shown to be efficient for patients with clival chordomas. Advances in knowledge: High-dose proton beam radiotherapy using a hyperfractionation scheme yielded a more favourable outcome than previous reports.