Functionalization of poly(vinylidene fluoride-co-hexafluoro propylene) (HFP) is made to prepared membrane for its application in fuel cell. The sulphonation of HFP membrane is carried out under control condition to maintain its stiffness and toughness of the membrane. The evidence of functionalization (sulphonation) is confirmed through different spectroscopic techniques such as NMR, FTIR, EDS mapping and UV-visible measurement and the degree of sulphonation is calculated from the integral peak area. The structural change from the usually crystallized alpha-phase to piezoelectric gamma-phase in functionalized membrane is established through XRD studies. Mechanical and thermal stabilities of the membrane are established through universal testing machine and thermogravimetric measurements. Suitability of proton exchange membrane has been verified through their high water uptake (12%), low fuel permeability (4.43 x 10(-7) cm(2)s(-1)) and thermal stability (up to 200 degrees C). The proton conductivity is found to be high in functionalized membrane while its low fuel permeability and high temperature stability is very good as compared to standard Nafion membrane. Efficiency of the membrane is reported in the form of selective parameter (ratio of conductivity and methanol permeability) of value 0.78 x 10(5) S cm(-3).s for functionalized HFP against the value of 0.81 x 10(5) S cm(-3).s for standard Nafion 117. Moderately high open circuit voltage (0.63 V) and power density of 48.34 mW/cm(2) is reported indicating very good performance of the overall membrane for direct methanol fuel cell. Therefore, direct functionalization of a polymer is a better approach for the preparation of fuel cell membrane.