Perfluorinated sulfonic acid ionomers have been extensively studied in particular for application to polymer electrolyte fuel cells as they show high proton conductivity at relatively low humidity. While vibrational spectroscopic methods have been successfully applied to investigate dissociation and hydration of their acid sites, the bands in the measured spectra have still been empirically assigned to local vibrations. We performed vibrational analysis of model compounds of the side chains of perfluorinated sulfonic acid ionomers by hybrid DFT calculation. On the basis of mean absolute errors in bond lengths and vibrational frequencies of triflic acid (CF3SO3H) calculated with various hybrid functionals and basis sets, PBE0/6-311G* the best results within affordable computational times and was applied for the model compounds. Most of the observed bands in the ATR-IR spectra of the model compounds were successfully reproduced by calculation of their dissociated sulfonate anions. New assignments were proposed for characteristic two peaks at around 970 and 1060 cm(-1) as combinations of SO3 symmetric stretch and adjacent CCO bend in two opposite phases. Vibrational bands of doubly hydrogen-bonded acid dimer were also identified in the IR spectrum of "as-received" PFEESA which was not hydrated. These results would provide a new basis for application of vibrational spectroscopy of perfluorinated sulfonic acid ionomers on their structural changes with degree of hydration.