An endoscope system comprises multiple types of treatment tools including a treatment-tool insertion unit, and a function unit having a function for performing treatment; an electrically-driven operation device which electrically drives the function unit; an electrically-driven advance/retreat device which electrically drives the treatment-tool insertion unit; a control device including at least one of a control unit for outputting a control signal to the electrically-driven advance/retreat device and the electrically-driven operation device, and an operating program corresponding to a treatment tool; and an operation instructing device including a first operating instruction unit for outputting an instruction signal for placing the electrically-driven operation device and the electrically-driven advance/retreat device into a manually-driven operating state, and a second operating instruction unit for outputting an instruction signal for placing the electrically-driven operation device and the electrically-driven advance/retreat device into a programmed-control state by the operating program. When receiving either of the signal from the first operating instruction unit or the signal from the second operating instruction unit, the control unit performs control for outputting the control signal corresponding to the received signal to at least one of the electrically-driven advance/retreat device and the electrically-driven operation device.