Abstract Analysis of performance of fuel cell is carried out by considering non-fluorinated electrolyte and variety of potential electrodes. The study spans low temperature regions and carried out MD investigation of transport of ions in a novel PEM fuel cell (PEMFC), which is composed of electrodes and SPEEK as a non-fluorinated electrolyte. Typical values of ion conductivity σ near room temperature are σ = 8.5 × 10−2 S cm−1 when Pt is used as electrode, σ = 26 × 10−2 S cm−1 when Pd3Ag is used as electrode, and σ = 0.34 × 10−2 S cm−1 when Pd is used as electrode. Thus, this study reveals a twofold implications. Firstly, the choice of electrolyte affects whether the traditional Pt electrode remains to be superior for the overall fuel cell performance. Secondly, using SPEEK electrolyte has a potential to yield a closely matching ion conductivity with the one obtained from the costly Nafion electrolyte.