Li-S batteries still suffer from two of the major challenges: polysulfide shuttle and low inherent conductivity of sulfur. Here, we report a facile way to develop a bifunctional separator coated with fluorinated multiwalled carbon nanotubes. Mild fluorination does not affect the inherent graphitic structure of carbon nanotubes as shown by transmission electron microscopy. Fluorinated carbon nanotubes show an improved capacity retention by trapping/repelling lithium polysulfides at the cathode, while simultaneously acting as the “second current collector”. Moreover, reduced charge-transfer resistance and enhanced electrochemical performance at the cathode-separator interface result in a high gravimetric capacity of around 670 mAh g−1 at 4C. Unique chemical interactions between fluorine and carbon at the separator and the polysulfides, studied using DFT calculations, establish a new direction of utilizing highly electronegative fluorine moieties and absorption-based porous carbons for mitigation of polysulfide shuttle in Li-S batteries.