In this research, molecular dynamics (MD) simulation was performed to explore the proton conductivity performance of three different sulfonated polybenzimidazole (SPBI) polymers with the same backbone but different functional groups as proton exchange membranes. To date, there are a few published experimental works on different SPBI polymer membranes. However, those studies were in profound disagreement about the positive effect of pendant functional groups attached to the backbone on PBI performance; therefore, MD simulations were required to resolve the conflicts. By comparisons of the simulated solubility parameter and glass transition temperature with the experimental measurements, it was initially determined that a simulation box made up of three chains of the polybenzimidazole polymer-each comprising of 30 monomers-was an appropriate simulation box for amorphous materials. Additionally, mean square displacement was used to analyze the dynamics of the self-diffusion coefficients. The calculated diffusion coefficients were 2.0 x 10-6, 1.4 x 10-6, and 1.1 x 10-6 cm2/s for PBI-S (SO3H PBI), PBI-PS (propylsulfonate PBI), and PBI-AS (arylsulfonate PBI), respectively. Based on the results, it was understood that the simulated proton conductivities were comparable with the results obtained by some researchers and consequently against other conflicting claims. The calculated proton conductivities are 13.1, 7.8, and 5.7 mS/cm for PBI-S, PBI-PS, and PBI-AS, respectively. Moreover, the examination of the free volume in the SPBI membranes revealed that the hydronium ion transport is compatible with the Cohen-Turnbull model. Ultimately, by analyzing the radial/angular distribution functions and water clusters, a novel assessment of a potential proton conduction pathway completed the investigation. The findings imply that proton hopping via water cluster connections is feasible.