A capsule medical device guidance system 1 includes a first magnetic field gradient setting unit 46 that obtains 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 a capsule medical device 10 in a liquid substantially zero as a first magnetic field gradient and a magnetic field setting unit 48 that causes, when guidance instruction information is not inputted by an operation input unit 7, a magnetic field generator 2 to apply the magnetic field having the first magnetic field gradient and causes, when guidance instruction information is inputted by the operation input unit 7, the magnetic field generator 2 to apply a magnetic field having the first magnetic field gradient added with a magnetic field gradient set in accordance with the guidance instruction information that is inputted by the operation input unit 7.
