According to a method and an apparatus for manufacturing a membrane-electrode assembly of the present invention, positioning holes are formed through a multi-layered lamination of an electrolyte membrane, electrodes, and sub-gasket films, in an area which is not included in a final product, and manifold holes of the membrane-electrode assembly are then quickly and accurately formed on the basis of the positioning holes. Therefore, the present invention can increase the productivity while lowering the defect rate of the membrane-electrode assembly.