To provide a paper sheet processing system and a control method therefor for recognizing a header card number and a new header card number with a hand scanner to reissue, when a paper sheet processing apparatus in which the header card is used can not recognize the header card number.

An unread header card CA is accumulated in a reject stacker 80. The unread header card CA (old header card) is removed and read with the hand scanner. Then, a header card CM1 is taken out from a group of header cards CM1 to CMn prepared for reissuing and is read with the hand scanner. A main controller 500 transmits the old header card number and the new header card number to a host PC600 to allow update. As the result, it becomes possible to reprocess with the paper sheet processing apparatus by using the new header card CM1.