Progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS) are neurodegenerative disorders associated with corticobasal degeneration pathology. A previous study evaluated white matter (WM) alteration using diffusion tensor imaging; however, the details are unclear due to the crossing fiber. This study evaluated cross-sectional and longitudinal WM changes in PSP and CBS using fixel-based analysis. This study also demonstrated consistent cross-sectional and longitudinal WM degeneration with previous histopathological studies and higher sensitivity than classical magnetic resonance imaging findings in differentiating PSP and CBS. Our results suggest that FBA can be a biomarker to classify PSP and CBS and estimate disease progression.