A heat treatment apparatus for a fuel cell membrane-electrode assembly is provided. The heat treatment apparatus includes a hot press installed on upper and lower sides of feeding path to move in the vertical direction on a frame and which presses the electrode catalyst layers on upper and lower surfaces of the membrane-electrode assembly sheet. A plurality of gripper modules are installed at set intervals in a base member along a feeding direction of the membrane-electrode assembly sheet, and selectively grip both side edges of the membrane-electrode assembly sheet. A driving unit reciprocally moves the base member in a direction perpendicular to the feeding direction of the membrane-electrode assembly sheet and in the feeding direction of the membrane-electrode assembly sheet.