A first glass substrate, a die including a penetrating space, a seat member, and a punching member are set so as to be arranged in this order. Subsequently, the seat member is punched by the punching member to remove part from the seat member through the penetrating space of the die. The part removed, is placed on the first glass substrate by the punching member so as to allow the part to serve as at least one spacer. Thereafter, the second glass substrate is placed on the first glass substrate with the at least one spacer in-between to form a glass panel unit.