A membrane-electrode junction agent, a proton conducting membrane having a junction layer, a membrane-electrode assembly, a polymer electrolyte fuel cell, and a manufacturing method of the membrane-electrode assembly, which enhance the power generation performance, realize the high fuel barrier property, and are capable of enhancing the joint strength between the membrane and the electrodes, is provided. A membrane-electrode junction agent that joins a proton conducting membrane and electrodes arranged on both surfaces of the proton conducting membrane to each other, the membrane-electrode junction agent including: a cross-linked compound (X) having a silicon-oxygen bond; a polymer material (Y) containing an acid group; and a hydrophilic resin (Z) containing no acid group.