An endoscope system that reduces a false color in a halation region when generating a display image in which a tone reflects a calculated image obtained by using two images obtained by imaging an observation target by using different illumination light beams at different timings, a processor device, and a method for operating the endoscope system are provided. An endoscope system 10 includes an image acquiring unit 54 that acquires a first image and a second image, the first image being obtained by using first illumination light, the second image being obtained by using second illumination light at a different timing from the first image； a halation-region detecting unit 74 that detects a halation region； a calculated-image generating unit 73 that performs calculation by using the first image and the second image and that generates a calculated image； a display-image generating unit 77 that generates a display image in which a tone reflects the calculated image； and a tone changing unit 75 that changes the tone of the halation region in the display image.
