An endoscope system includes a light source unit that emits first and second narrow band light simultaneously or alternately, a color filter in which first and second filters having different spectral characteristic are disposed, an image pickup device that receives light passing through the first filter in a first pixel group and receives light passing through the second filter in a second pixel group, and can set an exposing period and a reading period of an electric signal for each pixel, and a control unit that, when causing the first and the second narrow band light to be emitted alternately from the light source unit, synchronizes the emitting period of the first narrow band light, the exposing period of the first pixel group, and the reading period of the second pixel group in a first period, and synchronizes the emitting period of the second narrow band light, the exposing period of the second pixel group, and the reading period of the first pixel group in a second period.
