This paper studies the transport phenomena inside the electrolyte of proton exchange membrane fuel cells (PEMFCs) using atomistic simulation techniques. The investigated material of the electrolyte is Nafion®, which is the most widely adapted polymer membrane in low-temperature fuel cells. The molecular dynamics simulation system includes part of the Nafion structure, numerous water molecules, and the transporting cations. The cations are assumed to be hydroxoniums (H3O+), which are a hydrogen proton combined with a water molecule. Simulation results indicated that the electrostatic energy dominated the other potential energies in the total internal energy analysis. Clusters of water molecules tend to move toward the sulfonic acid group in the Nafion fragment, where the hydrophilic/hydrophobic characteristics can be observed. The transport phenomena of hydroxoniums are classified into two categories—continuous migration and noncontinuous hopping. The self-diffusion coefficients of the hydroxoniums and the water molecules in the membrane were evaluated to be 3.476×10−5cm2∕s and 4.993×10−5cm2∕s respectively, based on the Einstein relation. The calculated self-diffusion coefficients are of the same order of magnitude as the experimental results, which indicates this atomistic simulation is reaching more and more practical in engineering analysis.