Provided is an endoscope system capable of preventing a detection target from being overlooked in the case of using an automatic detection function for the detection target, and an operation method for the endoscope system. A comparison processing unit 74 performs comparison processing of comparing first-diagnosis identification information acquired at a first diagnosis with second-diagnosis identification information acquired at a second diagnosis that is different from the first diagnosis. A notification control unit 76 performs, if a determination is made that there is a difference in a detection target between the first diagnosis and the second diagnosis as a result of the comparison processing, control to make a notification about an oversight of the detection target.
