Sulfonation of polyetheretherketones (PEEK) was carried out in order to fabricate commercial perfluorosulfonic acid membrane alternatives, which were characterized in terms of their ion exchange capacity, ionic conductivity, water swelling, methanol crossover and electrochemical performance in their direct application as a methanol fuel cell. A high ion exchange capacity, 1.88, was achieved with a sulfonation reaction time of 8 h, with a significantly low methanol crossover low compared to that of Nafion. However, the morphological stability was found to deteriorate for membranes with sulfonation reaction times exceeding 8 h. Electrochemical cell tests suggested that the fabrication parameters of the membrane electrode assembly based on the sulfonated PEEK membranes should be optimized with respect to the physicochemical properties of the newly prepared membranes.