Provided is an endoscope system that can prevent an overlook of a detection target when an automatic detection function of a detection target is used, and an operation method thereof. The comparison processing section (74) performs a comparison process between the first diagnosis identification information acquired at the time of the first diagnosis and the second diagnosis identification information acquired at the time of the second diagnosis different from the first diagnosis. The notification control unit (76) performs control for notifying that the detection target has been overlooked when it is determined as a result of the comparison processing that there is a difference in the detection target between the first diagnosis and the second diagnosis.検出対象の自動検出機能を用いる場合において、検出対象の見落としを防止することができる内視鏡システム及びその作動方法を提供する。比較処理部（７４）は、第１診断時に取得した第１診断時識別情報と、第１診断時と異なる第２診断時に取得した第２診断時識別情報との比較処理を行う。報知制御部（７６）は、比較処理の結果、第１診断時と第２診断時において検出対象の差異があると判定された場合に、検出対象の見落としを報知する制御を行う。
