The thermostability and wettability of a separator play key roles in improving the safety and electrochemical properties of lithium-ion batteries (LIBs). Poly(ether ether ketone) (PEEK) exhibits excellent thermostability, and fluorinated polymers show improved wettability. However, the use of a fluorinated poly(ether ether ketone) (FPEEK) as a separator for LIBs has not been reported until now. In this work, a series of FPEEK polymers were successfully synthesized and further fabricated into porous LIB separators by an electrospinning method for the first time. The structure, thermal stability, morphology, mechanical strength, liquid electrolyte uptake, porosity, contact angle, ionic conductivity and electrochemical performance of the FPEEK separators were investigated. The FPEEK separators showed much stronger anti-shrinkage properties than the commercial polypropylene separator at 150 °C over 1 h. The FPEEK separator also exhibited superior electrolyte uptake (559%), strong mechanical properties (27.7 MPa), high porosity (88%), and great ionic conductivity (3.12 mS cm−1). More importantly, the cell assembled with this FPEEK separator presented outstanding cycle and C rate performances. The discharge capacity retention of the cell was 85.4% after 300 cycles at 60 °C. Hence, the obtained FPEEK separator improved the safety and electrochemical properties of the corresponding LIB.