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Background Function after acute stroke using the modified Rankin Scale (mRS) is usually assessed at a point in time. The analytical implications of serial mRS measurements to evaluate functional recovery over time is not completely understood. We compare repeated‐measures and single‐measure analyses of the mRS from a randomized clinical trial. Methods and Results Serial mRS data from AFFINITY (Assessment of Fluoxetine in Stroke Recovery), a double‐blind placebo randomized clinical trial of fluoxetine following stroke (n=1280) were analyzed to identify demographic and clinical associations with functional recovery (reduction in mRS) over 12 months. Associations were identified using single‐measure (day 365) and repeated‐measures (days 28, 90, 180, and 365) partial proportional odds logistic regression. Ninety‐five percent of participants experienced a reduction in mRS after 12 months. Functional recovery was associated with age at stroke <70 years; no prestroke history of diabetes, coronary heart disease, or ischemic stroke; prestroke history of depression, a relationship partner, living with others, independence, or paid employment; no fluoxetine intervention; ischemic stroke (compared with hemorrhagic); stroke treatment in Vietnam (compared with Australia or New Zealand); longer time since current stroke; and lower baseline National Institutes of Health Stroke Scale & Patient Health Questionnaire‐9 scores. Direction of associations was largely concordant between single‐measure and repeated‐measures models. Association strength and variance was generally smaller in the repeated‐measures model compared with the single‐measure model. Conclusions Repeated‐measures may improve trial precision in identifying trial associations and effects. Further repeated‐measures stroke analyses are required to prove methodological value. Registration URL: http:// www.anzctr.org.au ; Unique identifier: ACTRN12611000774921.