Disclosed herein is a stamping apparatus for biochips and a method of operating the stamping apparatus. The apparatus includes a table, a first chip table, a second chip table, a stamping unit and a control unit. The first chip table is provided on the table. A first biochip is seated onto the first ship table. A second biochip is seated onto the second chip table. The stamping unit is mounted to the table and operates the second chip table such that a surface of a junction of the second biochip seated on the second chip table is joined to a surface of a junction of the first biochip seated on the first chip table. The control unit controls operation of the first chip table or the second chip table.