Abstract INTRODUCTION The presymptomatic phase of frontotemporal dementia and amyotrophic lateral sclerosis associated with C 9orf72 repeat expansion features widespread structural brain changes. We aimed at fulfilling the unmet need of quantitative magnetic resonance imaging (MRI)‐derived measures suitable for disease tracking. METHODS We compared the profile of longitudinal gray (GM) and white matter (WM) changes in 66 presymptomatic carriers and 52 controls over 3‐year follow‐up and appraised their annualized rate of change (ARC). RESULTS Both putamen ( p < 0.01) and left insula ( p = 0.005) volumes declined the most in carriers over 40, with an ARC up to four‐fold higher than in controls. Increases in mean diffusivity occurred first in the left uncinate fasciculus, followed by thalamo‐cortical bundles ( p < 0.05), associated with higher neurofilament levels. DISCUSSION Our study highlighted the GM and WM structures showing the greatest longitudinal decline during the preclinical stage, whose ARC may serve as an MRI‐derived biomarker for longitudinal surveillance and therapeutic outcome. CLINICAL TRIAL REGISTRATION NCT02590276 and NCT05358431. Highlights We studied longitudinal multimodal MRI changes in presymptomatic C9orf72 disease. Carriers displayed faster atrophy in putamen, insula and cerebellar regions. Mean diffusivity increased mainly in uncinate and thalamo‐cortical tracts. These differences were even more significant in older (> 40) participants. We proposed targeted annualized rate of change as a quantitative biomarker.