Proton conduction is a ubiquitous phenomenon found in various fields of science. Especially, proton conduction in constrained systems such as biological membranes, electrolyte membranes plays an important role in the functionality of such systems. However, details of the proton conduction process in the constrained systems have not yet been elucidated. Here we present results of first-principles molecular dynamics simulations carried out to reveal the nature of proton conduction in a representative polymer electrolyte membrane (PEM), Nafion. Our simulations demonstrate that features of the proton conduction mechanisms previously proposed are not correct. For example, in the low water content membrane, the previously proposed mechanism explains that protons migrate as H₃O⁺ bonded to H₂O while our simulations reveal that proton hopping occurs substantially even in the low water content membrane. Based on the results of the simulations, we propose a new mechanism of proton conduction that is highly consistent with the experimental observations. Conclusions derived from the present study provide a solid scientific basis for the development of the next-generation PEMs.