Quaternized polymers as ionomeric binders in the electrode enable the operation of alternative fuel cells under high pH conditions or anhydrous conditions to overcome the challenges of the proton exchange membrane fuel cells. Hydrophobicity of the ionomers derived from high fluorine content is beneficial to electrode performance, but due to the synthetic difficulties, not many fluorinated quaternized ionomers have been reported with their influence on electrode behavior in these emerging fuel cells. In this presentation, we report a series of quaternized poly(fluorene)s with controlled hydrophobicity by changing the length of flexible fluoroalkyl chains. The contact angle of the electrodes containing the ionomers ranged from 108.7 to 163.8°, comparable to that of the perfluorosulfonic acid-bonded electrodes. The anion exchange membrane fuel cells employing the ionomer exhibits improved durability (voltage loss 0.41 mV h⁻¹) through better water management. The high-temperature proton-exchange membrane fuel cell using the ionomer showed superior H₂/air performance (1.4 A cm^-2 at 0.4 V). The study of the fluorinated poly(fluorene) highlights the benefits of hydrophobic ionomers for highly efficient and cost-effective fuel cell systems.