Provided are an endoscope system, a processor device for an endoscope system, and a method for operating the endoscope system that can suppress a decrease in frame rate without reducing the brightness and resolution of an oxygen saturation image. In the special observation mode, the first illumination light and the first illumination light are different from each other in spectral characteristics, and the second illumination light including different absorption wavelength lights having different absorption coefficients between oxyhemoglobin and reduced hemoglobin is turned off. The sample is alternately irradiated through the image sensor, and imaging is performed with a CMOS image sensor. The first imaging signal is read from the image sensor during the extinguishing period after irradiation of the first illumination light, and the second imaging signal is read from the imaging element during the extinguishing period after irradiation of the second illumination light. At this time, the second readout time required for reading the second imaging signal is shorter than the first readout time required for reading the first imaging signal. An oxygen saturation image is generated based on the first and second imaging signals read from the imaging element.酸素飽和度画像の輝度及び解像度を低下させずに、フレームレートの低下を抑えることを可能とする内視鏡システム、内視鏡システムのプロセッサ装置、及び内視鏡システムの作動方法を提供する。特殊観察モード時には、第１照明光と、第１照明光とは分光特性が異なり、かつ、酸化ヘモグロビンと還元ヘモグロビンとで吸光係数が異なる異吸光波長光を含む第２照明光とを、消灯期間を介して交互に検体に照射させ、ＣＭＯＳ型の撮像素子により撮像を行う。第１照明光の照射後の消灯期間に撮像素子から第１撮像信号を読み出し、第２照明光の照射後の消灯期間に撮像素子から第２撮像信号を読み出す。このとき、第１撮像信号の読み出しに要する第１読み出し時間より、第２撮像信号の読み出しに要する第２読み出し時間を短くする。撮像素子から読み出された第１及び第２撮像信号に基づいて酸素飽和度画像を生成する。
