A method for fabricating a seal-integrated separator for a fuel cell is presented, with which seals can be accurately positioned and the assembling time for the fuel cells may be greatly reduced. The method comprises the steps of: providing an upper mold having a groove positioned corresponding to second and fourth seals disposed on one side of a separator body, and a lower mold having a groove positioned corresponding to first and third seals disposed on the other side of the separator body; holding the separator body between the upper mold and the lower mold; and injecting melted seal material to form the seals into each of the grooves in the upper mold and the lower mold through separate gates respectively formed in the upper and lower molds. Through this method, a seal-integrated separator having the first to fourth seals which are integrated on both sides of the separator body is fabricated.