FA patients exhibited significantly reduced cerebellar gray matter volume compared to controls (p = 0.024) after intracranial volume correction, skin-to-cerebellum distance did not differ between groups (p = 0.11). Stepwise linear regression analysis disclosed that the anterior cerebellar gray matter volume was a significant predictor of SARA improvement (β = −0.18, p < 0.001) and the posterior cerebellar gray matter volume of CCAS-S improvement (β = −0.13, p 0.023). Neither SCP diameter nor skin-to-cerebellum distance significantly impacted ctDCS efficacy. Cerebellar gray matter volume is associated to ctDCS-induced symptoms improvements in FA.