The present invention provides a method for manufacturing a composite separator for a polymer electrolyte membrane fuel cell. The method comprises: preparing a prepreg as a continuous carbon fiber-reinforced composite and a graphite foil; allowing the cut prepreg and graphite foil to pass through a stacking/compression roller to be compressed; allowing the prepreg in which the graphite foil is integrally stacked to be heated and pressed by a hot press such that hydrogen, air, and coolant flow fields are formed or to pass through a hot roller to be formed into a separator; removing unnecessary portions from the heated and pressed separator using a trim cutter; and post-curing the thus formed separator, wherein the graphite foil may be stacked on the prepreg as the continuous carbon fiber-reinforced composite such that a graphite layer is integrally formed with the prepreg.