We investigated the possibility to increase the working temperature and endurance of proton exchange membranes for fuel cells and water electrolyzers by thermal annealing of short side chain perfluorosulfonic acid (SSC-PFSA) Aquivion® membranes. The Ionomer nc Analysis (INCA method), based on nc/T plots where nc is a counter elastic force index, was applied to SSC-PFSA in order to evaluate ionomer thermo-mechanical properties and to probe the increase of crystallinity during the annealing procedure. The enhanced thermal and mechanical stability of extruded Aquivion® 870 (equivalent weight, EW = 870 g·mol−1) was related to an increase of long-range order. Complementary differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) measurements confirmed the increase of polymer stiffness by the annealing treatment with an enhancement of the storage modulus over the whole range of temperature. The main thermomechanical relaxation temperature is also enhanced. DSC measurements showed slight base line changes after annealing, attributable to the glass transition and melting of a small amount of crystalline phase. The difference between the glass transition and melting temperatures derived from INCA plots and the ionic-cluster transition temperature derived from DMA measurements is consistent with the different experimental conditions, especially the dry atmosphere in DMA. Finally, the annealing procedure was also successfully applied for the first time to an un-crystallized cast membrane (EW = 830 g·mol−1) resulting in a remarkable mechanical and thermal stabilization.