In this study, a new type of modified Nafion membrane containing sulfonated poly(ether ether ketone) (SPEEK) nanofibers was fabricated for proton exchange membrane fuel cells. The solution blowing method was used for fabrication of SPEEK nanofibers, which were impregnated into Nafion solution to form pore-filled composite membranes with different contents of SPEEK nanofibers. The performance of the composite membranes as proton exchange membranes was investigated and compared with Nafion 117. The results showed that the introduction of SPEEK nanofibers into the Nafion matrix significantly improved its thermal stability, proton conductivity, swelling rate and selectivity. The maximum value of the proton conductivity of 0.09 S cm⁻¹ was obtained when the nanofiber content was 10 wt% at 20 °C and 100% RH, higher than that for Nafion 117 (0.083 S cm⁻¹). It is indicated that solution blown nanofibers are a kind of promising filler material for enhancing the performance of Nafion membranes, and the composite membrane containing SPEEK nanofibers can be considered as a novel proton exchange membrane for fuel cell applications.