This study determined whether the Functional Independence Measure (FIM) and the Frenchay Activities Index (FAI) could be used together as a more comprehensive score to assess the activities of daily living (ADL) in stroke survivors. Subjects were recruited from stroke patients consecutively admitted to the inpatient neurology or rehabilitation department at a university hospital in southern Taiwan. We interviewed 209 first stroke survivors at least 1 year after stroke onset during their clinical visits, at home, or in long-term care institutions. Combinations of FIM and FAI as a comprehensive assessment of ADL were measured. All items of the FIM and the FAI were included in a non-parametric factor analysis to determine their underlying constructs. Two comprehensive functional independence scores were then computed as functions of the FIM and FAI scores. The distributional characteristics of the comprehensive scores were examined. Approximately 90% of the total variation was explained by three factors. One single factor comprised all the items from FIM, while the FAI items loaded on two other factors, suggesting that FIM supplements FAI without overlap in content. We further demonstrated that the presence of ceiling or floor effects when either the FIM or the FAI was used could be removed using combined scores of the two instruments. The FIM and the FAI assessed different domains with good construct validity. A comprehensive assessment of functional independence obtained by combining the FIM and the FAI scores is potentially more appropriate and useful for clinical and research applications in stroke patients.