A method of manufacturing a fuel cell separator, the method including: subjecting the peripheral surfaces other than the respective gas passages of a pair of separator substrates formed from stainless steel to a cathodic electrolytic treatment within an alkali solution, thereby forming an iron-based hydrated oxide film on the peripheral surfaces of the pair of separator substrates (S200), conducting a water treatment by wetting the surface of the iron-based hydrated oxide film with water (S202), performing electrodeposition coating of an electrocoating material containing an aqueous resin onto at least one of the water-treated iron-based hydrated oxide films provided on the pair of separator substrates (S204), and baking the aqueous resin obtained by electrodeposition coating (S206).