There are provided an endoscope system, a processor device, and an operation method of an endoscope system, which can verify afterward whether or not pre-imaging has been performed under appropriate conditions. An endoscope system has an oxygen saturation calculation unit that calculates the oxygen saturation of an observation target using an LUT. The endoscope system includes: an image acquisition unit that acquires a correction image obtained by imaging the observation target before calculating the oxygen saturation； an oxygen saturation correction amount calculation unit that calculates an oxygen saturation correction amount with respect to the oxygen saturation using the correction image； an oxygen saturation correction unit that corrects the oxygen saturation calculated by the oxygen saturation calculation unit according to the oxygen saturation correction amount； and a storage unit that stores the correction image and an oxygen saturation image, which shows the oxygen saturation after correction, so as to be associated with each other.
