Soluble quaternary ammonium functionalized poly(fluorenyl ether)s (PFEQAs) with a wide range of ion exchange capacities (IECs) were successfully synthesized from a novel tertiary amine group containing cardo monomer. Complete conversion of tertiary amine group to quaternary ammonium group was established, which enables precise control over IEC of the resultant polymers by adjusting monomer-loading ratio. The influence of IEC on the thermal stability, mechanical integrity, water uptake and ion conductivity of the PFEQAs were investigated. Furthermore, four counter ions were selected and their influences on the water uptake and ion conductivity of PFEQAs were studied in detail in order to give a comprehensive view of the transport properties of these anion exchange membranes. It was observed that the water uptakes of the membranes with different counter ions followed the trend: OH− > SO42− > Cl− > I− while their ion conductivities followed another trend: OH− > SO42− > Cl− > I−. These membranes exhibited promising characteristics for anion exchange membrane water electrolyzers working with neutral PH water with or without supporting electrolytes.