Linear perfluoropolyether (PFPE) peroxide was used to confer superhydrophobic surface properties to gas diffusion layer (GDL) by means of direct functionalization of a GDL based on carbon cloth (CC) material. The thermal decomposition of a linear PFPE peroxide produces linear PFPE radicals that covalently bond the unsaturated moieties on the surface. Perfluorinated radicals are directly and covalently bound to the carbonaceous structure of the CC without any spacer that could decrease both thermal and chemical stability of the GDL. The obtained CC hydrophobicity exceeded the superhydrophobicity threshold and was enduringly stable. The relationship between the linkage of fluorinated chains and the variations of surface chemical-physical properties were studied combining X-ray photoelectron spectroscopy (XPS), resistivity measurements, scanning electron microscopy (SEM) and contact angle measurements. Despite the excellent insulating properties of the PFPE polymer, the functionalized carbonaceous materials substantially retained their conductive properties. The PFPE-modified GDLs were tested in a single fuel cell at the lab scale. The cell tests were run at two temperatures (60°C and 80°C) with a relative humidity (RH) of hydrogen and air feeding gases equal to 80/100% and 60/100%, respectively.