A paper sheet counting system includes: a first paper sheet counting apparatus whose operation mode can be switched between a cooperative mode and an independent mode, the first paper sheet counting apparatus including: a first receiving unit configured to take in deposited paper sheets one by one; at least two first stacking units configured to stack therein the paper sheets; a first recognition unit configured to recognize and count the paper sheets; and a first transport unit configured to transport the paper sheets between the first receiving unit and the first stacking units, based on a recognition result of the first recognition unit; a second paper sheet counting apparatus whose operation mode can be switched between a cooperative mode and an independent mode, the second paper sheet counting apparatus being capable of communicating with the first paper sheet counting apparatus, the second paper sheet counting apparatus including: a second receiving unit configured to take in deposited paper sheets one by one; at least one second stacking unit configured to stack therein the paper sheets; a second recognition unit configured to recognize and count the paper sheets; and a second transport unit configured to transport the paper sheets between the second receiving unit and the second stacking unit, based on a recognition result of the second recognition unit; and a tallying unit configured to acquire count results from the first recognition unit and the second recognition unit and to tally the count results, when the first paper sheet recognition unit and the second paper sheet recognition unit are in the cooperative modes.