There are provided an endoscope system, a processor apparatus for an endoscope system, and a method for operating an endoscope system with which a decrease in the frame rate can be suppressed without a decrease in the brightness and resolution of an oxygen saturation image. In a special observation mode, first illumination light and second illumination light having a spectral property different from a spectral property of the first illumination light and including different-absorption-wavelength light that has different absorption coefficients for oxygenated hemoglobin and reduced hemoglobin are alternately emitted to a test body while a turn-off period is interposed, and an image is captured by a CMOS image sensor. A first image capture signal is read from the image sensor during the turn-off period after emission of the first illumination light, and a second image capture signal is read from the image sensor during the turn-off period after emission of the second illumination light. Here, a second read time taken to read the second image capture signal is made shorter than a first read time taken to read the first image capture signal. An oxygen saturation image is generated on the basis of the first and second image capture signals read from the image sensor.
