There are provided an endoscope system, a processor device, and an operation method of an endoscope system that can calculate an accurate oxygen saturation by reducing artifacts. An endoscope system includes: an oxygen saturation correction unit that calculates the amount of change in oxygen saturation in the latest second period with respect to the oxygen saturation in the past first period and that maintains a value of the oxygen saturation in the second period in a case in which the amount of change is less than a threshold value and corrects the oxygen saturation in the second period to a value obtained as a result of setting the amount of change to the threshold value in a case in which the amount of change is equal to or greater than the threshold value and an oxygen saturation image generation unit that generates an oxygen saturation image using the oxygen saturation in the second period.
