This capsule type medical device system includes: a position detection device 4 which detects the position within the living body of a capsule type medical device 2 which can be ingested to within the living body; an electrode 5 which is provided in the vicinity of the outer surface of the capsule type medical device 2, and which applies an electrical stimulus to living body tissue; and a control device 6 which controls the electric current which flows to the electrode 5; and the control device 6 controls the electric current which flows to the electrode 5 based upon positional information which is detected by the position detection device 4.