Background/Objectives: Little is known about the impact of myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) on brain atrophy. This multicenter longitudinal study compares brain MRI volumes and T2 lesion volume between MOGAD patients, relapsing-remitting MS (RRMS) patients and a healthy control (HC) group with brain MRI scans available from an online repository. Methods: In total, 16 adult MOGAD patients (9 F) were age- and sex-matched with 44 RRMS patients (17 F) recruited in Verona MS Center and 14 HC subjects. The availability of two brain MRI scans performed 18 ± 6 months apart was mandatory for each patient. Annual percentage brain volume change (PBVC/y), baseline global brain, white matter (WM), gray matter (GM) regional brain volumes and T2 lesion volume were compared between groups. Results: PBVC/y was lower in MOGAD than in RRMS patients (p = 0.014) and lower in HC subjects than in MS patients (p = 0.005). Overall, MOGAD showed higher mean global brain (p = 0.012) and WM volume (p = 0.024) but lower median T2 lesion volume at timepoint 1 (p < 0.001); T2 lesion volume increased over time in the RRMS (p < 0.001) but not in the MOGAD cohort (p = 0.262). Conclusions: The structural brain MRI features of MOGAD show higher global brain and WM volumes and lower brain volume loss over time compared to RRMS, suggesting different underlining pathogenetic mechanisms.