Cell voltage at high current densities (HCD) of an operating proton-exchange membrane fuel cell (PEMFC) suffers from losses due to the local-O2 and bulk-H+ transport resistances in the cathode catalyst layer (CCL). Particularly, the interaction of perfluorosulfonic acid (PFSA) ionomer with the carbon supported platinum catalyst plays a critical role in controlling reactant transport to the active site. In this study, we perform a systematic analysis of the side chain length and equivalent weight (EW) of PFSA ionomers on the CCL transport resistances. Ex situ measurements were carried out to quantify the ionomer characteristics such as the molecular weight, proton conductivity and water uptake. Nanomorphology of ionomers cast as 60-120 nm thin-films is characterized using grazing-incidence X-ray scattering. In situ fuel cell electrochemical diagnostic measurements were carried out to quantify the reactant (H+/O2) transport properties of the CCL. Ionomer EW was found to play a major role with decreasing EW yielding higher proton conductivity and water uptake that led to lower bulk-H+ and local-O2 transport resistances in the CCL. Finally, a 1D-semi-empirical performance model has been developed to quantify the impact of ionomer EW on cell voltage loss factors.