A capsule medical device guiding system and a magnetic field generating device that allow a capsule medical device, which is constrained on a liquid surface, to be smoothly submerged into a liquid. A capsule medical device guiding system 1 of the present invention incudes a capsule endoscope 10 that includes a permanent magnet and is configured to be introduced into a liquid in a subject, a magnetic field generating unit 2 configured to generate a magnetic field to be applied to the permanent magnet to guide the capsule endoscope 10 and configured to change a direction of the generated magnetic field in a three-dimensional space, and a magnetic field controller 43 configured to cause the magnetic field generating unit 2 to generate a variable magnetic field including a direction varying magnetic field whose magnetic field direction varies periodically on a plane whose direction changes periodically about a vertical axis and which is other than a horizontal plane, and a magnetic field for generating a magnetic attracting force for moving the capsule endoscope 10 vertically downward.
