Objectively measured physical activity volume serves as a predictive factor for functional recovery in patients with stroke. Malnutrition, a frequent complication of stroke, may influence the relationship between physical activity and functional recovery. This study aimed to examine the association between physical activity volume and functional recovery in patients with stroke, stratified by their nutritional status. This multicenter prospective observational study included 209 patients with stroke admitted to two Japanese convalescent rehabilitation hospitals. Participants were categorized based on the geriatric nutritional risk index (GNRI) at admission [≥92, high GNRI group ( n = 133); <92, low GNRI group ( n = 76)]. Physical activity levels were measured as the duration of total physical activity (TPA), which is the sum of light-intensity physical activity and moderate-to-vigorous physical activity, using a triaxial accelerometer during the first 7 days after admission. Outcome measures are represented as the relative gain of the motor score on functional independence measure (M-FIM effectiveness) during the first month after admission. The multiple regression analysis, adjusting for age, sex, comorbidity, onset to admission intervals, motor paralysis, initial M-FIM, and cognitive FIM, showed that the duration of TPA in the first 7 days was significantly associated with the M-FIM effectiveness over the first month in both low GNRI [ B = 0.12, 95% confidential intervals (CI) = 0.01; 0.24, P = 0.049] and high GNRI group ( B = 0.11, 95% CI = 0.01; 0.21, P = 0.027). This study demonstrates a positive predictive association between early TPA level and functional recovery in stroke patients, irrespective of their nutritional status.