PROBLEM TO BE SOLVED: To provide an endoscope system capable of improving visibility of an observation target when a pigment is sprayed onto the observation target, and an operation method of the endoscope system.SOLUTION: With a use of a syringe, a pyoktanin pigment is sprayed in a mist form onto an observation target from a tip of a spray tube inserted into a forceps channel of an endoscope. A light source emits red light LR, green light LG, blue light LB and violet light LV, which are illuminated via a light path connection part, a light guide and an illumination lens to the observation target. The pyoktanin pigment has a light absorption characteristic of absorbing the green light LG. An imaging element in the endoscope has red pixels, green pixels and blue pixels whose exposure times can be changed color by color. An imaging control part controls imaging timing of the imaging element such that an exposure time Tof the green pixels is longer than an exposure time Tof the red and blue pixels.SELECTED DRAWING: Figure 9