An endoscope system includes a processor configured to generate a clock at predetermined timing, a light source apparatus configured to irradiate white light and excitation light in a time division manner in synchronization with the clock, and an endoscope configured to perform image pickup based on irradiation timing of the light source apparatus. The processor generates a first white light image at a first clock, generates a first fluorescent image at a second clock, generates a second white light image at a third clock, and generates a third white light image at a fourth clock and superimposes the second white light image and the first fluorescent image at the fourth clock and superimposes the third white light image and the first fluorescent image at a fifth clock.