Ion-conducting polymers are important materials for a variety of electrochemical applications. Perfluorinated ionomers, such as Nafion, are the benchmark materials for proton conduction and are widely used in fuel cells and other electrochemical devices including solar-fuel generators, chlor-alkali cells, and redox flow batteries. While the behavior of Nafion in bulk membranes (10 to 100s mu m thick) has been studied extensively, understanding its properties under thin-film confinement is limited. Elucidating the behavior of thin Nafion films is particularly important for the optimization of fuel-cell catalyst layers or vapor-operated solar-fuel generators, where a thin film of ionomer is responsible for the transport of ions to and from the active electrocatalytic centers. Using a combination of transport-property measurements and structural characterization, this work demonstrates that confinement of Nafion in thin films induced thickness-dependent proton conductivity and ionic-domain structure. Confining Nafion films to thicknesses below 50 nm on a silicon substrate results in a loss of microphase separation of the hydrophilic and hydrophobic domains, which drastically increases the material's water uptake while in turn decreasing its ionic conductivity.