An encapsulated medical device guidance system, and a method of controlling the system, in which guidance coils are arranged to divide a magnetic field generating plane into at least two front and rear areas, a magnetic field for canceling gravity applied to a capsule endoscope itself is formed, and superposed on a magnetic field for moving or changing an attitude, a frictional resistance in moving a capsule endoscope is reduced by decreasing an area of an endoscope to contact the surface of an intracavital.