An image pickup system includes a light emitting section that emits light for illuminating an object which operates periodically, an image pickup section including an image pickup device that performs an image pickup operation by a rolling shutter system, a period detection section that detects a period of motion of the object, a light emission signal generating section that outputs a stroboscopic light emission signal for causing the light emitting section to perform a stroboscopic light emission in synchronism with the period of the motion, a light emission period control section that sets as a light emission permission period, and a light emission non-permission period, and a light emission control section that performs control for causing the light emitting section to perform a light emission in the light emission permission period, and performs control for inhibiting a light emission of the light emitting section in the light emission non-permission period.