There are provided an endoscope system, a processor apparatus for an endoscope system, and a method for operating an endoscope system with which the brightness and S/N of a normal observation image obtained in a special observation mode can be increased. In the special observation mode, second illumination light including different-absorption-wavelength light that has different absorption coefficients for oxygenated hemoglobin and reduced hemoglobin is emitted, a turn-off state is thereafter initiated, and signal reading is performed for some of a plurality of pixel rows in accordance with a skip read method. Subsequently, first illumination light, which is normal light, is emitted, a turn-off state is thereafter initiated, and signal reading is performed for all of the pixel rows in a column direction in accordance with a pixel addition read method. An image processor generates an oxygen saturation image on the basis of a second image capture signal read in accordance with the skip read method and a first image capture signal read in accordance with the pixel addition read method, and generates a normal observation image on the basis of the first image capture signal.
