A banknote handling apparatus includes: a plurality of storing units 52 configured to store a banknote; a transport unit 18 configured to transport the banknote having been put into a machine body 2 to each of the storing units 52; a recognition unit 40 disposed at the transport unit 18 and configured to read out a serial number of the banknote having been put into the machine body 2; and a control unit 70 configured to control the transport unit 18. The control unit 70 controls the transport unit 18 such that the banknote whose serial number has been read out by the recognition unit 40 and the banknote whose serial number has not been read out by the recognition unit 40 are stored into different storing units 52.