The present disclosure relates to a cell stacking apparatus for a second battery and a system for manufacturing a secondary battery. The cell stacking apparatus includes a grip part configured to hold and move an electrode-separator assembly having a plurality of positive electrode plates and a plurality of negative electrode plates, in which each of the plurality of positive electrode plates and each of the plurality of negative electrode plates are respectively bonded to opposing surfaces of a separator, and a stacking part including a stack plate movable in a cell stacking direction. The stacking part is configured to fold and stack the electrode-separator assembly on the stack plate, and to move the stack plate downward to fold the electrode-separator assembly in zigzags when the grip part holds and moves the electrode-separator assembly to the stack plate.