Provided are an endoscope system, an endoscope system processor device, and an endoscope system operation method, such that it is possible to improve signal-to-noise ratio and the reliability of an oxygen saturation image. First and second illumination light with different spectral characteristics are projected alternately on a subject with a blackout period interposed therebetween. During each blackout period, a signal read-out of G pixels from an image capture element (39) is carried out without carrying out pixel addition, and a signal read-out of B pixels and R pixels is carried out with pixel addition carried out. By comparing, on the basis of the G pixel signals, first image capture signals which are read out from the image capture element during the blackout periods after the projections of the first illumination light and second image capture signals which are read out from the image capture element during the blackout periods after the projections of the second illumination light, a position deviation is computed between images based on the first and second image capture signals. On the basis of the position deviation, an alignment of images between the first and second image capture signals is carried out, and an oxygen saturation image is generated on the basis of the aligned first and second image capture signals.
