We have used coarse-grained simulation methods to investigate the effect of stretching-induced structure orientation on the proton conductivity of Nafion-like polymer electrolyte membranes. Our simulations show that uniaxial stretching causes the hydrophilic regions to become elongated in the stretching direction. This c hange has a strong effect on the proton conductivity, which is enhanced along the stretching direction, while the conductivity perpendicular to the stretched polymer backbone is reduced. In a humidified membrane, stretching also causes the perfluorinated side chains to tend to orient perpendicular to the stretching axis. This in turn affects the distribution of water at low water contents. The water forms a continuous network with narrow bridges between small water clusters absorbed in head group multiplets. In a dry membrane the side chains orient along the stretching direction.