The effect of Nafion-clay nanocomposite membranes on hydrogen and methanol crossover in a proton exchange membrane (PEM) fuel cell was studied. Several analytical methods were used to determine the fuel crossover rate and the ionic conductivity of the membranes. It is the first time a Nafion-clay nanocomposite was investigated to reduce the hydrogen migration rate across the PEM membrane. The Nafion-clay nanocomposites demonstrated significantly reduced permeability to both methanol and hydrogen. The reduction of hydrogen and methanol crossover was compared, and the possible mechanistic difference was discussed. The ionic conductivities for both in-plane and through-plane were measured using alternating current impedance techniques. The ionic conductivities of the Nafion-clay nanocomposites were lower than a pure Nafion membrane of the same thickness.