This study proposed to evaluate the temporal trend, define the minimal clinically important difference (MCID) for five functional status measures, and identify risk factors for reaching deterioration in the MCID. This prospective cohort study analyzed 680 patients with ischemic stroke and 151 patients with hemorrhagic stroke at six hospitals between April 2015 and October 2021. All patients completed the functional status measures before rehabilitation (baseline), and at the 12th week and 2nd year after rehabilitation. Patients in the post-acute care (PAC) group exhibited significantly larger improvements for the functional status measures compared to those in the non-PAC group (p < 0.05). Patients with hemorrhagic stroke also displayed larger improvements in the functional status measures when compared to patients with ischemic stroke. Furthermore, the improvement in MCID ranged from 0.01 to 16.18 points when comparing baseline and the 12th week after rehabilitation, but the deterioration in MCID ranged from 0.38 to 16.12 points. Simultaneously, assessing the baseline and the second year after rehabilitation, the improvement in MCID ranged from 0.01 to 18.43 points, but the deterioration in MCID ranged from 0.68 to 17.26 points. Additionally, the PAC program, age, education level, body mass index, smoking, readmission within 30 days, baseline functional status score, use of Foley catheter and nasogastric tube, as well as a history of previous stroke are significantly associated with achieving deterioration in MCID (p < 0.05). These findings suggest that if the mean change scores of the functional status measures have reached the thresholds, the change scores can be perceived by patients as clinically important.