Partially fluorinated poly(fluorenyl ether ketone)s with different degree of sulfonation were successfully synthesized by the sulfonation of the designed parent polymer. The sulfonation took place only at the specific (2, 7)-position on the fluorenyl groups due to the positions adjacent to the ether bond occupied by methyl groups. The sulfonated polymers are soluble in common organic solvents and can readily be cast into tough and smooth films from their solutions. The properties of proton conductivity, water uptake, thermal and oxidative stability for the membranes were investigated. It was found that the oxidative stability of the membrane decreased with increasing the degree of sulfonation. However, the partially fluorinated membrane with high degree of sulfonation exhibited better oxidative stability compared to the non- fluorinated analogy with low degree of sulfonation. The proton conductivity of the membranes increased with increasing the degree of sulfonation and temperature. Moreover, the membranes also showed good thermal and hydrolytic stabilities.