Multiple system atrophy-cerebellar type (MSA-C) exhibits faster disease progression than does hereditary spinocerebellar degeneration (hSCD). In this study, we aimed to investigate the differences in the treatment effects and sustainability of intensive rehabilitation between patients with hSCD and those with MSA-C. Forty-nine patients (hSCD = 30, MSA-C = 19) underwent a 2- or 4-week intensive rehabilitation program. Balance function was evaluated using the scale for the assessment and rating of ataxia (SARA) and the balance evaluation systems test (BESTest) at pre-intervention, post-intervention, and 6-month follow-up. Notably, both groups demonstrated beneficial effects from the rehabilitation intervention. However, differences were observed in the magnitude and duration of these effects. In the hSCD group, the SARA scores at follow-up remained similar to those at baseline, indicating sustained benefits. However, the MSA-C group showed some deterioration in SARA scores compared with baseline scores but maintained improvements on the BESTest, demonstrating partial sustainability. Differences, mainly in sustainability, were observed between the hSCD and MSA-C groups. This may be due to varying rates of symptom progression. The findings of this study are significant when considering the frequency of follow-ups based on disease type.