A new process for manufacturing a perfluorinated polymer electrolyte for proton-conducting membranes of fuel cells is presented. The process is based on the aqueous emulsion copolymerization of tetrafluoroethylene (TFE) with perfluoro(3,6-dioxa-4-methyl-7-octene) sulfonyl fluoride (FS-141) and characterized by a high productivity, reduced consumption of the expensive sulfonated monomer, and the possibility of controlling the equivalent weight (EW) of the resulting copolymer. The copolymers are characterized by a uniform composition in combination with optimal EW values and afford the synthesis of proton conducting membranes for fuel cells with properties comparable with those of commercial Nafion membranes. A mechanism of the copolymerization of TFE with FS-141 in an aqueous emulsion is proposed and confirmed by kinetic and topochemical data.