A flexible composite membrane with homogeneously distributed zirconia and titania was prepared using sulphonated polystyrene ethylene butylene polystyrene (SPSEBS) and commercial zirconia and titania. The composite membranes of SPSEBS up to 10 wt% zirconium dioxide and titanium dioxide content were prepared. The study was oriented towards the optimization of the synthesis and characterization of such composite membranes to choose the best inorganic composition in terms of thermal stability and proton conductivity. The proton conductivity of the composite membrane was measured using electrochemical impedance spectroscopy (EIS). The thermogravimetric analysis (TGA) analysis of the composite membranes showed better thermal stability than SPSEBSmembrane and at the same time, higher content (wt.%) of inorganic material decreased the proton conductivity. A good adhesion between inorganic domains and the polymer matrix was confirmed through morphology studies such as scanning electronmicroscopy (SEM) and atomic forcemicroscopy (AFM). The methanol permeability and selectivity ratio were decreased with increasing inorganic materials. The feasibility of these hybrid membranes as proton conducting electrolyte in proton exchange membrane fuel cell (PEMFC) was investigated and results were compared with that of commercialNafion 117membrane. The single fuel cell test showed that the fuel cell with homogeneous composite membrane showed better performance under the fuel cell operating condition.