A capsule guiding system includes: an electrode pad arranged outside a human body to perform human body communication with a capsule endoscope and detect at least one of position and direction of the capsule endoscope; a magnetically guiding device which moves the capsule endoscope; a detector which detects a relative position between the electrode pad and the magnetically guiding device; a calculator which calculates at least one of the position and direction of the capsule endoscope based on a detection value of the electrode pad, and calculates at least one of an absolute position and direction of the capsule endoscope with respect to the magnetically guiding device based on at least one of the position and direction of the capsule endoscope and the relative position detected by the detector; and a control unit which controls the magnetically guiding device based on at least one of the absolute position and direction.