A surface treatment apparatus and a surface treatment system having the same are disclosed. The surface treatment apparatus includes a process chamber in which the surface treatment process is conducted, a plasma generator for generating process radicals as a plasma state for the surface treatment process, the plasma generator being positioned outside of the process chamber and connected to the process chamber by a supply duct, a heat exchanger arranged on the supply duct and cooling down temperature of the process radicals passing through the supply duct and a flow controller controlling the process radicals to flow out of the process chamber. The flow controller is connected to a discharge duct through which the process radicals are discharged outside the process chamber. The plasma surface treatment process is conducted to the package structure having minute mounting gap without the damages to the IC chip and the board.