Proton exchange membrane fuel cell (PEMFC) arepromising to become the next generation of energyconversion devices that are efficient, lightweight, andhave clean emissions and used extensively to convertchemical energy of hydrogen fuel to electricity. In these cells, a hydrated polymer membrane acts asan electrolyte layer through which protons travel [۱].Although the perfluorosulfonic acid type of polymers such as Nafion have attracted enormousattention from the polymer electrolyte membrane fuel cell. The drawbacks of this PFSA-basedpolymers such as high cost, drastic decrease in proton conductivity with dehydration, and poor fuelcrossover in direct methanol fuel cell have also stimulated another intensive study in developing non-PFSA-based polymers especially sulfonated hydrocarbon-based polymers like sulfonated poly (etherether ketone) (SPEEK), sulfonated poly(styrene) (SPS), and sulfonated poly(benzimidazole). SPEEKhas been known as one of the promising candidates for fuel cell application since it has high thermooxidativestability and extraordinary mechanical properties as well as high-cost effectiveness [۲].In addition, Due to the complex nature of the membranes used, the optimization of fuel cellperformance is a difficult task and relies on a number of factors. The molecular dynamics (MD) is aparticularly powerful tool for studying PEMFCs, as it provides the computational efficiency to studylength and time scales relevant to these systems [۱]. There is two most important approach in MDsimulation. In all atom MD (AAMD) simulations, the total forces on all the atoms are calculated, andthen the dynamics of designed systems are simulated by discrete integration of Newton’s equations ofmotions with a shorter timescale to determine the movement of atom’s response to forces while the coarse-grained MD (CGMD) reduces the number of degrees of freedom in a system, by reducing thenumber of interaction sites, resulting in a computationally less expensive model than the equivalentfully atomistic model [۳]. This review presents results from several computational papers that usemolecular dynamics, which explicitly describe proton transport in poly (ether ether ketone) used inPEMs. Table ۱ has a brief information related to MD studies on proton transport in PEEK membraneand FC applications.The results presented demonstrate the role of number of chains and monomers, water content (λ), forcefields and methods. After all, It should be noted the importance of the interaction betweenhydronium and the charged side chains and effect of morphology on the performance of PEMFC. As aconclusion, MD results of density and solubility parameter of these simulations confirm that themolecular dynamics simulation is a good and reliable method to investigate the effect thatmolecular structure of polymer chain and water concentration have on transportation of proton.