The development of high-performance low-cost membrane materials is crucial for application in proton exchange membrane fuel cells (PEMFCs). In this study, two types of poly(alkyl–fluorene isatin)-based proton exchange membranes (PEMs) are designed and prepared successfully via facial superacid-catalyzed Friedel–Crafts polycondensation. The fluorene-based polymers exhibit good solubility and film-forming ability, and the produced PEMs possess excellent mechanical properties, dimensional stability, and oxidization stability because of the aromatic backbone. Atomic force microscopy showed that HFxDPy-PS-based PEMs have more significant phase separation structures than MFxDPy-PS-based PEMs due to the longer soft alkyl chains on the fluorene groups. HF3DP1-PS exhibits high proton conductivity that reached 88.56 mS cm −1 at 80 °C. The H 2 /O 2 single fuel cell assembled with HF3DP1-PS exhibits a power density of 753 mW cm −2 , which is close to that of a fuel cell with commercial Nafion 212 (774 mW cm −2 ) under the same conditions. All these results indicate the broad potential application of poly(alkyl–fluorene isatin)-based PEMs in PEMFCs. • Poly(alkyl-fluorene isatin)-based PEMs with pendant sulfonate groups are designed and synthesized. • The produced PEMs possess excellent physical and chemical properties. • The single fuel cell with HF3DP1-PS exhibits a power density of 753 mW cm −2 .