Background To date, little is known about the presence and extent of cerebellar cortical pathology in early stages of MS. Objective The aims of this study were to (i) investigate microstructural changes in the normal-appearing cerebellar cortex of early MS patients by using 7 T MRI and (ii) evaluate the influence of those changes on clinical performance. Methods Eighteen RRMS patients and nine healthy controls underwent quantitative T₁ and T₂* measurement at 7 T MRI using high-resolution MP2RAGE and multi-echo gradient-echo imaging. After subtracting lesion masks, average T₁ and T₂* maps were computed for three layers in the cerebellar cortex and compared between groups using mixed effects models. Results The volume of the cerebellar cortex and its layers did not differ between patients and controls. In MS patients, significantly longer T₁ values were observed in all vermis cortical layers and in the middle and external cortical layer of the cerebellar hemispheres. No between-group differences in T₂* values were found. T₁ values correlated with EDSS, SDMT and PASAT. Conclusions We found MRI evidence of damage in the normal-appearing cerebellar cortex at early MS stages and before volumetric changes. This microstructural alteration appears to be related to EDSS and cognitive performance.