An apparatus for manufacturing a membrane-electrode assembly for a fuel cell is provided. The apparatus includes a sub-gasket feeding unit that forms first electrode windows, unrolls a first sub-gasket sheet, and supplies the sheet to a transfer line. An electrode membrane loading unit installed over the transfer line forms electrode catalyst layers on both faces of an electrolyte membrane, collects the electrode membrane sheet cut, and loads the sheets onto first electrode windows. A sub-gasket loading unit installed over the transfer line forms second electrode windows, collects a second sub-gasket sheet, and loads the sheets on the electrode membrane sheet. MEA bonding units installed on the transfer line bond the first sub-gasket sheet, the electrode membrane sheet, and the second sub-gasket sheet mutually stacked while passing the first sub-gasket sheet, the electrode membrane sheet, and the second sub-gasket sheet between a pair of hot rollers along the transfer line.