A capsule medical device guidance system includes a capsule medical device including a magnetic field responding unit and introduced into a subject, a magnetic field generator that generates a magnetic field for the responding unit to guide the device; an operation input unit for inputting operation information for magnetically guiding the device; a storage unit that stores position/posture information about position or posture of the device in an guidance region; an input unit for inputting setting instruction information for setting the position/posture information as a mark indicating a position to which the device is returned in the region, and return instruction information for returning the device to the mark; and a control unit that controls the generator to guide the device based on the operation information, and makes the generator generate the magnetic field to the mark based on the stored position/posture information in response to the return instruction information.