Renewable energy production from fuel cells and energy storage in flow batteries are becoming increasingly important in the modern energy transition. Both batteries use polyelectrolyte membranes (PEMs) to allow proton transport. In this chapter, both PEMs and PEMs-based nanocomposites have been discussed using various simulational approaches. A coarse-grained model of a Nafion film capped by the substrates with variable wettability has been used to simulate nanocomposites of PEMs by classical molecular-dynamics (MD) method. Classical MD modeling results have also been reviewed for a PEM-graphene oxide nanocomposite internal structure and dynamics. Ab-initio simulations have been implemented to describe the proton transfer pathways in anhydrous PEMs. Finally, the large-scale mesoscopic simulations have been introduced to shed light on the water domain features present in the hydrated PEMs. A brief description of polybenzimidazole membrane as electrolyte and Ionic Liquids as dopants for fuel cells is also presented.