A new series of polymer composite membranes was fabricated using a linear sulfonated poly(ether ether ketone) (SPEEK) polymer with zinc cobalt oxide (ZCO) as an inorganic filler and evaluated for fuel cell applications. SPEEK was obtained by the direct sulfonation of PEEK using concentrated sulfuric acid, and appropriate quantities of ZCO were loaded into it to yield the polymer composites. Proton nuclear magnetic resonance studies revealed the degree of sulfonation of SPEEK to be 55%, while morphological studies confirmed the successful incorporation of inorganic fillers into the polymer matrix. To evaluate the suitability of the prepared composite membranes for fuel cell applications, their physicochemical properties were studied in detail. The pristine SPEEK membrane exhibited a proton conductivity of 0.009 S cm−1 at 30°C, whereas the values for the composite membranes loaded with 2.5 to 10 wt% of ZCO were in the range 0.012–0.020 S cm−1. Moreover, the composite membranes showed excellent thermal stability up to 370°C. Indeed, the membranes obtained by the incorporation of ZCO into the SPEEK polymer show potential for fuel cell applications.