A series of new sequenced sulfonated naphthalenic polyimides were synthesized containing a flexible aromatic–aliphatic diamine. The obtained membranes present the advantage of being soluble in N-methyl pyrrolidone (NMP) which is a less toxic solvent than the previously used m-cresol. In this work, we report on the solvent and acidification method effects on the properties of the membranes such as density, water uptake, proton conductivity as well as on the performance of these membranes in fuel cell operation. The membranes prepared from NMP solution and acidified with ion-exchange resins give the best results. They have good mechanical properties as well as high ionic conductivity (14.4×10−2 Scm−1 at 80°C) and good performances as proton exchange membrane (PEM) in fuel cell at 70°C.