There are provided a substrate transferring apparatus for continuously loading/unloading a plurality of substrates in and from a process chamber to reduce time spent on transferring the substrates and to improve productivity and a substrate processing system using the same. The substrate transfer apparatus is installed in the transfer chamber and transfers substrates between first and second process chambers which is positioned lateral sides of the transfer chamber and a load rock chamber. The substrate transfer apparatus includes a driving unit to supply a rotational force, a spindle connected to the driving unit, first swivel plate arms to load/unload substrate to/from first process chamber, and second swivel plate arms to load/unload substrate to/from second process chamber. Since substrates before and after being processed are rapidly exchanged during the simultaneous or continuous process of plural substrates, processing rate increases and overall productivity can be increased.