Aim To assess the effect of age‐adjusted Charlson Comorbidity Index (CCI) score on Functional Independence Measure (FIM) score gain in older rehabilitation patients. Methods This prospective cohort study observed 306 older rehabilitation patients admitted to a secondary hospital between February and April 2015. Groups were compared using CCI score cut‐offs of ≤4, 5–6 and ≥ 7. Results Complete FIM data were available for 280 patients. The mean age‐adjusted CCI score was 5.59 ± 1.96. An age‐adjusted CCI score ≤4 correlated with higher FIM scores at admission P = 0.015, and discharge P = 0.002, but not with a greater gain in FIM score P = 0.067. There were no significant between‐group differences in mortality, hospital transfers or length of stay. Conclusion The Charlson age‐comorbidity index was not a prognostic marker for FIM gain. Age and comorbidity alone are not barriers to the rehabilitation of older patients.