Perfluorinated sulfonic acid (PFSA) ionomers have high proton conductivity and excellent mechanical-chemical stability under humid conditions in low temperature Polymer Electrolyte Membrane Fuel Cell (PEMFC) application. In this work, we compare performance and durability between long side chain (LSC) and short side chain (SSC) PFSA ionomers as a solid electrolyte membrane and as ionomer-additive in the electrodes. Membrane electrode assemblies (MEAs) are prepared combining the LSC/SSC membrane with the corresponding LSC/SSC ionomer in the catalyst layer. Thereby, their chemical compatibility could be determined. MEAs are tested in single cell test benches with segmented bipolar plate for long term degradation test with dynamic load-cycling. While maintaining uniform conditions, we have experienced that different MEAs show different behavior in short-term to long-term application. Owing to its stability in lower equivalent weight; SSC ionomer provides favorable proton conductivity leading to higher power density of the cell. Nevertheless, faster degradation of SSC than the LSC ionomer are encountered in this study likely due to the higher gas permeation of thinner SSC membranes and lower polytetrafluoroethylene content. This study contributes a significant insight in the behavior of ionomers in FC as function of time, and shows avenues for further improvement of durability.