Provided are an endoscope system, a processor device, and a method for operating the endoscope system that can identify, more easily and more accurately than in the related art, a region in which an index value cannot be accurately calculated and a region in which the index value can be accurately calculated. An endoscope system 10 includes: an image acquiring unit 54 that acquires an endoscope image obtained by imaging an observation target； a baseline information calculating unit 82 that calculates baseline information (operation value "Z") by using the endoscope image, the baseline information being information about light scattering characteristics or light absorbing characteristics of the observation target and information that is at least not dependent on particular biological information； a region setting unit 83 that sets, by using the baseline information, a calculation region in which the index value is to be calculated, the index value indicating a state of the observation target； and an index value calculating unit 84 that calculates the index value in the calculation region set by the region setting unit 83, by using the endoscope image.
