This work addresses the study of the effect of ultrasonic (US) treatment on the properties of alcohol solutions of perfluorinated sulfonic acid polymer Nafion® and cast membranes. The effect of the duration of US treatment on the physico-chemical properties (water uptake, transport and mechanical properties) of the resulted membranes is described for the first time. Upon the US treatment, viscosity of the polymer solutions irreversibly decreases due to deagglomeration and rupture of macromolecular chains. As a result of the US treatment, mechanical properties of the Nafion® membranes are deteriorated. The dependences of water uptake and conductivity of the Nafion® membranes in the proton form on sonication time pass the maximum (at 30–45 min). Due to the sonication of polymer solutions, proton conductivity of the membranes increases by 40–45%. Upon extended sonication, the content of sulfonic acid groups decreases, and carboxyl groups are formed at the ends of macromolecules. Thus, water uptake of the membranes prepared from the polymer solutions after the US treatment for 60 min decreases, and conductivity of the obtained membranes in the H+-form is reduced. However, for the Nafion® membranes in the Na+-form, as the duration of the US treatment is extended, their conductivity and diffusion permeability tend to increase due to the enhanced connectivity of pores and channels as well as due to the participation of carboxyl groups in the ionic transport. Upon extended sonication, selectivity of the cation transfer through the membranes is reduced. The results of this work highlight the importance of the proper selection of favorable conditions of the US treatment of the solutions of perfluorinated sulfonic acid polymers for the preparation of hybrid membranes and for the development of catalytic layers of membrane-electrode assemblies for fuel cells.