A banknote handling apparatus includes: a first winding storage unit; a second storage unit; a transport unit; a recognition unit; and a control unit. The first storage unit stores the banknotes, while providing a mark associated with inventory amount information of the first storage unit. To perform a reconciliation process for the first storage unit, the control unit allows some of the banknotes stored in the first storage unit to be fed from the first storage unit, based on the mark, for recognition by the recognition unit, and determines an inventory amount of the first storage unit based on a result of the recognition and the inventory amount information associated with the mark.