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This study aimed to investigate the relationship of Functional Independence Measure for motor function (FIM-M) with sarcopenia, and physical activity in patients with stroke undergoing rehabilitation. This cross-sectional study included patients with stroke at a single convalescent rehabilitation hospital. Sarcopenia was diagnosed based on the Asia Working Group for Sarcopenia 2019 criteria. Physical activity was measured as the duration of light-intensity physical activity and moderate to vigorous physical activity using a triaxial accelerometer. Of 80 patients (median age: 72.0 years), 46 (57.5%) were diagnosed with sarcopenia. In multivariate linear regression analysis, FIM-M score was significantly associated with sarcopenia (β = −0.15, p = .043) and light-intensity physical activity (β = 0.55, p < .001). In another model, FIM-M score was significantly associated with moderate to vigorous physical activity (β = 0.27, p = .002) but not with sarcopenia. This study demonstrated that FIM-M was partially associated with sarcopenia and associated with physical activity regardless of intensity in patients with stroke.