Given the increase in stroke-related social costs, studies on survival and functional prognosis after stroke are urgently needed. Therefore, we investigated the relationship between the frequency of rehabilitation treatments in the acute and subacute phases of stroke and the long-term mortality of stroke survivors with mild-to-moderate disabilities. We performed a retrospective cohort study using data from the Korean National Health Insurance Service database. Our final cohort included 733 patients with national disability registration grades 4–6. The number of special rehabilitation treatment claim codes was used as a proxy for the frequency of rehabilitation treatments. Furthermore, we categorized the rehabilitation frequencies within 24 months of stroke onset as 1–50, 51–200, 201–400, and >400. The dependent variable was all-cause mortality, and it was evaluated from 24 to 84 months after stroke onset. Severe disability was associated with a lower long-term mortality rate in the chronic phase (p< 0.001). In the Cox regression analysis, severe disability, older age, male sex, and chronic kidney disease were independent risk factors for long-term mortality in patients with stroke and mild-to-moderate disabilities. However, the frequency of acute/subacute rehabilitation treatments did not significantly improve long-term mortality. Our results suggest that the association between rehabilitation frequency and lower long-term mortality for patients with mild-to-moderate stroke was inconclusive. Therefore, further study is needed to determine a better-customized rehabilitation treatment system for these patients.