The positron annihilation lifetime (PAL) technique was used to investigate the yield and lifetime of positronium (Ps) in three different samples of per‐fluorinated sulfonic acid/polytetrafluoroethylene (PTFE) proton exchange membranes. The high probability of Ps formation enables the study of the hole volume size by the PAL technique and explains the mechanism of both methanol permeation and proton conductivity of the membranes in relation to the relative humidity (RH). The influence of various membrane parameters, including water uptake, proton conductivity, and mechanical properties, was studied. The concentration of water molecules and SO3−–H3O+groups is correlated with the ion exchange capacity (IEC) of the membranes where higher IEC leads to high absorbance of water. The proton conductivity is enhanced by increasing the IEC value of the membrane. The activation energies of decomposition temperature for the F‐950 membrane are the lowest (Eb = 2.856 and 1.030 eV for the 1st and 2nd decomposition peaks, respectively, implying that the membrane with high IEC is thermally less stable. With increasing the IEC of the membranes, the concentration of the water molecules/SO3 group increases. In addition, the proton conductivity of the membrane is positively influenced by increasing water content at high RH. The fact that the variations in hole volume size and both methanol permeability and proton conductivity are highly dependent on RH suggests that hole volume size plays an important role in many parameters of hydrated perfluorinated sulfonic acid/PTFE proton exchange membranes. The outcomes data were introduced and interpreted appropriately with a theoretical model and compared with the literature.