Ion-containing polymers, in particular Nafion, are a critical component in hydrogen fuel cells, where they are not only used as the proton conducting membrane but also as the ion conducting binder within the catalyst layer. Within the catalyst layer, Nafion is often confined to thicknesses on the order of ten nanometers or less. It is well reported that many physical properties of polymers deviate from their bulk like behavior when confined on length scales comparable to the size of the molecule, typically 10s of nanometers. The mechanical properties of the ionomer are of particular importance due to the swelling response to changes in hydration level. In this work, we have implemented a cantilever bending technique to investigate the swelling induced stresses in Nafion thin films as a function of humidity. We have found a significant influence of the film thickness on the swelling stresses as well as the Young’s modulus when the films are thinner than 50 nm; and the apparent increase in stiffness translates to a decrease in water content. Although the modulus of the film strongly depends on the processing and annealing conditions, the relative thickness dependence is independent of annealing. In addition to thermal annealing, hygrothermal aging and substrate interactions have also been observed to have a large influence on the thickness dependent mechanical behavior. The changes observed in the mechanical response are correlated to structural and chemical changes in the film shown by neutron and x-ray scattering as well as the IR absorption spectra.