In this work, we report the inscription of fiber Bragg grating through the over-clad in cyclic transparent fluoropolymer (CYTOP) optical fiber using a phase mask technique and a 400 nm femtosecond pulsed laser. 8 mm-long grating were obtained in less than 20 s with 500 <inline-formula><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula>W average beam power. To investigate the FBG properties and discriminate between the protective over-clad influence and the core-cladding effect, we inscribe FBGs in the fiber with and without the over-clad. We also show that the temperature sensitivity of CYTOP-FBGs with the over-clad depends on the relative humidity, whereas CYTOP-FBGs without the over-clad achieve almost zero sensitivity to humidity and sensitivity to temperature of 26.7 pm/<inline-formula><tex-math notation="LaTeX">$^{\circ }$</tex-math></inline-formula>C.