In recent years, clinical trial research on stroke intervention measures has been developing rapidly. In order to provide reliable conclusions, the outcome assessment of clinical trials is crucial. Tools for functional status evaluation have been widely adopted as outcome assessment, and have become mandatory for qualified clinical trials of stroke treatment. In this paper, the classification of functional assessment scales in stroke is reviewed, and the applications of functional assessment scales in clinical trials of stroke treatment are presented. National Institute of Health Stroke Scale, Barthel Index, and modified Rankin Scale are the top three frequently applied assessment scales in stroke trials. Also, their validity, reliability, responsiveness, and feasibility are described. Furthermore, analytical methods used to assess those functional assessments are highly heterogenous, while dichotomy of scale score is the most widely used. Although there is no consensus on designation of the functional assessment time, three-month is the most popular, reliable, and feasible choice in stroke trails.