An image pickup system 101 includes a light source unit configured to perform illumination with G illumination light, B illumination light, and B' illumination light； an image pickup unit 12 configured to pick up an image of return light from an object image for each predetermined period and output an image pickup signal； a pre-processing unit 31 configured to generate a first image signal, a second image signal, and a third image signal, each corresponding to one field, and sequentially output the image signals； and a synchronization processing unit 32 configured to selectively assign the image signals sequentially outputted to a first color channel, a second color channel, and a third color channel. The synchronization processing unit 32 switches first assignment processing for assigning the first image signal or the second image signal to the first to third color channels and second assignment processing for assigning the first image signal or the third image signal to the first to third color channels.
