Waterborne epoxy resin (WEP) has been widely used as an anti-corrosive coating for metals. However, it is still a big challenge to further improve its anti-corrosion performance due to the poor barrier properties to corrosive media. In this study, fluorinated graphene (FG) was used as a filler in WEP to improve its barrier properties, which contributes to corrosion resistance enhancement. The chemical composition and microstructures of FG and FG-modified WEP were systematically analyzed, and its corrosion resistance was also studied. Results reveal that the addition of FG sheet to WEP not only can significantly improve the tensile strength of WEP coating, but also increase the barrier properties of WEP coating and block the penetration of corrosive agent throughout the coating to the interface between coating and substrate. Meanwhile, the results also declare that the F content of FG has a significant effect on mechanical properties and long-term corrosion resistance, and the performance of FG-modified WEP coating will deteriorate with the increase of F content.