A membrane-electrode assembly manufacturing method comprising: a first step of preparing a membrane-electrode laminate comprising an electrolyte membrane having a first surface and a second surface opposite the first surface, a first electrode on the first surface, and a second electrode on the second surface; a second step of preparing a first sub-gasket film having a first central region and a first peripheral region surrounding the first central region; a third step of forming a first electrode window in the first central region; a fourth step of forming at least two first positioning holes in the first peripheral region; a fifth step of preparing a second sub-gasket film having a second central region and a second peripheral region surrounding the second central region; a sixth step of forming a second electrode window in the second central region; a seventh step of forming at least two second positioning holes in the second peripheral region; an eighth step of attaching the first sub-gasket film to the first surface of the electrolyte membrane such that at least a portion of the first electrode is exposed through the first electrode window and attaching the second sub-gasket film to the second surface of the electrolyte membrane such that at least a portion of the second electrode is exposed through the second electrode window, whereby forming a multilayer laminate; a ninth step of forming at least one manifold hole in a central portion of the multilayer laminate corresponding to the first and second central regions (131b, 132b); and a tenth step of removing a peripheral portion of the multilayer laminate corresponding to the first and second peripheral regions (131a, 132a), wherein the ninth step of forming the at least one manifold hole and the tenth step of removing the peripheral portion of the multilayer laminate are performed based on positions of the first and second positioning holes (PH1, PH2). a first step of preparing a membrane-electrode laminate comprising an electrolyte membrane having a first surface and a second surface opposite the first surface, a first electrode on the first surface, and a second electrode on the second surface; a second step of preparing a first sub-gasket film having a first central region and a first peripheral region surrounding the first central region; a third step of forming a first electrode window in the first central region; a fourth step of forming at least two first positioning holes in the first peripheral region; a fifth step of preparing a second sub-gasket film having a second central region and a second peripheral region surrounding the second central region; a sixth step of forming a second electrode window in the second central region; a seventh step of forming at least two second positioning holes in the second peripheral region; an eighth step of attaching the first sub-gasket film to the first surface of the electrolyte membrane such that at least a portion of the first electrode is exposed through the first electrode window and attaching the second sub-gasket film to the second surface of the electrolyte membrane such that at least a portion of the second electrode is exposed through the second electrode window, whereby forming a multilayer laminate; a ninth step of forming at least one manifold hole in a central portion of the multilayer laminate corresponding to the first and second central regions (131b, 132b); and a tenth step of removing a peripheral portion of the multilayer laminate corresponding to the first and second peripheral regions (131a, 132a), wherein the ninth step of forming the at least one manifold hole and the tenth step of removing the peripheral portion of the multilayer laminate are performed based on positions of the first and second positioning holes (PH1, PH2).