An electronic endoscope system including a light source unit alternately repeats irradiation and non-irradiation of illumination light while alternately switching illumination light to be irradiated between first and second illumination lights which is different from at least one of a light amount and a spectral property from the first illumination light； an image pickup device that captures a subject illuminated with the illumination light； and an image pickup device control that reads, during a non-irradiation period of the illumination light following an irradiation period of the illumination light, charges which have been accumulated in the image pickup device during the irradiation period, and wherein the irradiation period of the first illumination light and the second illumination light are set to have different lengths depending on at least one of a difference in light amount and a difference in spectral property between the first illumination light and the second illumination light.
