Provided are an endoscope system, a processor device, and a method of operating an endoscope system that performs warning in a case where correction of data used for calculation of oxygen saturation is a failure and reliably perform the correction of the data used for the calculation of the oxygen saturation. The endoscope system has an oxygen saturation calculation unit that calculates the oxygen saturation of an observation object, and includes an image acquisition unit that acquires a preliminarily captured image that is an image of the observation object, a correction unit that corrects an LUT that the oxygen saturation calculation unit uses for the calculation of the oxygen saturation, using the preliminarily captured image, a determination unit that determines a success or failure of the correction, and a warning unit that performs warning in a case where a determination result obtained by the determination unit is a failure.
