An endoscope system according to the present invention includes: an endoscope equipped with a long insertion portion; a medical instrument which includes a treating portion installed in a distal part and used to perform various treatments in a body cavity and a long sheath including a rigid portion with predetermined flexibility and a flexible portion more flexible than the rigid portion, the rigid portion and flexible portion being installed consecutively starting from a distal side, where the sheath is inserted in a channel of the insertion portion of the endoscope; an operation instruction apparatus used to give commands regarding operation of the medical instrument; a first medical instrument drive apparatus which operates the treating portion of the medical instrument; and a second medical instrument drive apparatus which moves the sheath forward and backward.
