A capsule medical device guidance system includes: a magnetic field generator that applies a magnetic field having a magnetic field gradient to the magnetic field response unit and guides the capsule medical device a first setting unit that sets a magnetic field gradient of a magnetic field for generating a vertical magnetic attracting force which makes a resultant force of a buoyancy of the capsule medical device and a gravity force and the vertical magnetic attracting force of the capsule medical device in the liquid substantially zero as a first magnetic field gradient an operation input unit to which guidance instruction information for guiding the capsule medical device by a magnetic field and moving the capsule medical device from a first position to a second position is inputted a second setting unit that obtains a magnetic field gradient of a magnetic field for generating a magnetic attracting force corresponding to the guidance instruction information inputted by the operation input unit and sets the obtained magnetic field gradient of the magnetic field as a second magnetic field gradient and a control unit that controls the magnetic field generator to continuously apply the magnetic field having the first magnetic field gradient set by the first setting unit and keep the capsule medical device in a static state in the liquid even if any specific operation is not inputted when the guidance instruction information is not inputted by the operation input unit and controls the magnetic field generator to apply a magnetic field having a magnetic field gradient obtained by adding the second magnetic field gradient set by the second setting unit to move the capsule medical device from the first position to the second position to a state in which the first magnetic field gradient set by the first setting unit to keep the capsule medical device in a static state in the liquid is continuously applied when the guidance instruction information is inputted by the opera
