Increasing physical activity (PA) is an important rehabilitation target for patients with sub-acute stroke during hospitalization in order to recover physical function and prevent stroke recurrence. However, the characteristics of low PA in stroke patients during hospitalization who were targets for increased intervention have not been reported. The purpose of this study was to investigate the relationship between the daily number of steps and physical function and quadriceps muscle thickness (QMT) in patients with sub-acute stroke during hospitalization for convalescence rehabilitation. Twenty-nine patients with ischemic or haemorrhagic stroke (mean age, 69 ± 11 years) hospitalized for inpatient convalescent rehabilitation were included. PA was measured using a three-dimensional accelerometer that calculates the daily number of steps taken. Physical function was measured by a short physical performance battery (SPPB; 0–12 points) and the leg motor selectivity score (6 motor stages defined by Brunnstrom), and the QMT of both legs was measured using ultrasonography. PA was significantly correlated with the SPPB score (r = 0.63, p = 0.0002), QMT on the paretic side (r = 0.41, p = 0.02), and QMT on non-paretic side (r = 0.56, p = 0.002). There were no significant effects of the leg motor selectivity score on daily PA (F = 1.37, p = 0.27). In the multiple regression analysis, only the SPPB score showed significant linear regression (β = 0.44, p = 0.02). PA in male patients with sub-acute stroke during hospitalization was related to physical function and QMT and not with the severity of paresis.