A method of manufacturing a fuel cell separator, includes: stacking a first separator plate and a second separator plate having first and second protruding portions so that the first and second protruding portions protrude in a direction away from the first separator plate, the first and second protruding portions being adjacent to both sides of a first junction portion to be joined to the first separator plate; pressing the first and second protruding portions toward the first separator plate so that the first junction portion is pressed against the first separator plate; and joining the first junction portion to the first separator plate while the first junction portion is being pressed against the first separator plate, wherein in the pressing, the first junction portion is pressed against the first separator plate by elastic deformation of a first bent portion bent between the first junction portion and the first protruding portion.