Mesoporous Santa Barbara Amorphous (SBA-15) was synthesized, and it was grafted with phosphonate functionality using a simple two-step process involving chloromethylation and subsequent phosphonation. The phosphonated SBA-15 (PSBA-15) was characterized using Fourier transform infra-red (FTIR) spectroscopy, solid-state 13C nuclear magnetic resonance (NMR), 29Si NMR, and 31P NMR for confirming successful modification. Morphology features were verified by small angle X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy TEM analyses. Poly(styrene-ethylene-butylene-styrene) (PSEBS) was chosen as the base polymer and phosphonic acid functional groups were grafted onto the polymer using the aforementioned approach, where chloromethyl (-CH2Cl) groups were attached to the main chain using Friedel Craft’s alkylation, followed by the phosphonation of the chloromethylated polymer by the Michaels-Arbuzov reaction resulting in phosphonated PSEBS (PPSEBS). The functionalization was confirmed using NMR and FTIR spectroscopy studies. Composite PPSEBS/PSBA-15 membranes were fabricated with different filler concentrations (2, 4, 6, and 8%) of PSBA-15. Various studies such as water uptake, ion exchange capacity, and the proton conductivity of the composite membranes were undertaken with respect to fuel cell applications. From the studies, it was found that the PPSEBS/PSBA-15 membrane with 6 wt% of filler exhibited maximum proton conductivity of 8.62 mS/cm at 140 °C. Finally, membrane electrode assembly (MEA) was fabricated using PPSEBS/6% PSBA composite membrane, platinium (Pt) anode, and Pt cathode, and was tested in an in-house built fuel cell setup. A maximum power density of 226 mW/cm2 and an open circuit voltage of 0.89 V were achieved at 140 °C under un-humidified condition.