Provided are an endoscope system capable of improving luminance and an S/N ratio of a normal observation image that is obtained in a special observation mode, a processor device of the endoscope system, and a method of operating the endoscope system.In a special observation mode, after first illumination light is radiated, some of a plurality of pixel rows of an imaging element (39) are reset en bloc. Illumination light is switched from the first illumination light to second illumination light, the second illumination light is radiated, and then, a turned-off state is reached. During this turn-off period, signal reading is sequentially performed from all pixel rows. An image processing unit (44) generates a normal observation image on the basis of a first imaging signal read from the pixel row exposed by the first and second illumination light without being subjected to resetting. Further, the image processing unit (44) generates an oxygen saturation image on the basis of a second imaging signal read from the pixel row subjected to the resetting and exposed by only the second illumination light, and the first imaging signal.
