Objective To analyze the association between the disease course， functional status， and hospitalization costs among stroke inpatients. Methods Using the medical record data of 445 stroke inpatients admitted to the Department of Rehabilitation Medicine， Xiangyang Central Hospital， Hubei Province from July 2023 to December 2023， an analysis was conducted on the relationships between the disease course， functional status， total hospitalization costs， and inpatient rehabilitation costs. Results Functional status was significantly and positively correlated with total hospitalization costs. Patients with the worst functional status had the highest costs （￥18，786.13）， and these costs were significantly higher than those of patients with the best functional status （Coef = 0.24， P < 0.001）. Meanwhile， no significant difference was found in rehabilitation costs among functional status groups. The disease course significantly influenced rehabilitation costs， with the group with a disease course of 121-180 days showing significantly higher rehabilitation costs than the group with a disease course of 0-30 days （Coef = 0.18， P = 0.015）， but it had no significant effect on total hospitalization costs. Subgroup analysis indicated that patients with moderate functional status were particularly sensitive to the disease course. Conclusions Functional status shows a positive correlation with total costs but has no correlation with rehabilitation costs. The disease course independently influences rehabilitation costs， and patients with moderate functional status are more sensitive to early rehabilitation.