A novel organic–inorganic mesoporous silica functionalized with perfluoroalkylsulfonic acid groups analogous to that of Nafion® has been prepared. A condensation reaction between surface silanol groups of the mesoporous silicas and 1,2,2-trifluoro-2-hydroxy-1-trifluoromethylethane sulfonic acid Beta-sultone was conducted. High proton conducting sulfonated poly(ether ether ketone) (sPEEK)/ functionalized mesoporous silica composite membranes were prepared through homogeneous dispersive mixing and solvent casting method. In the study, proton conductivity (σ) of composite membrane is increased from 0.01 to 0.038 (S/cm) as the modified mesoporous silica content is increased from 0 to 5 wt. %. It is found that the ion exchange capacity (IEC) is increased from 1.54 to 1.70 (meq/g) as the modified mesoporous silica content is increased from 0 to 5 wt. %. From morphology investigation, it is found that incorporation of modified mesoporous silica by rotary vacuum evaporation enables the preparation of homogeneous membranes. The membranes present a good adhesion between inorganic domains which could be used for fuel cell applications.