Provided is a valuable medium processing system capable of improving the work efficiency of a person in charge when continuously storing a quantity of valuable media collected from a plurality of valuable medium transaction machines into a storage unit. The valuable medium processing system comprises: a valuable medium processing machine for performing a count process on a predetermined kind of valuable media from among the valuable media collected from the valuable medium transaction machines; and a control machine for storing and managing the quantity of valuable media collected from the valuable medium transaction machines on a per valuable medium transaction machine basis. While the processing machine is performing the counting process on the valuable media collected from one of the valuable medium transaction machines, if the quantity of valuable media which are collected from a different valuable medium transaction machine and on which the processing machine cannot perform the counting process is inputted by an input operation means, the control machine controls a predetermined storage means to store the inputted quantity of valuable media as the quantity of valuable media collected from the different valuable medium transaction machine.