A system for guiding capsule medical device is provided with a capsule medical device, a magnetic guidance device, an operation input unit, a control device, and an image display device. The capsule medical device is includes therein a first and second imaging units that image images in imaging directions different from each other and a permanent magnet. The magnetic guidance device applies a magnetic field to the permanent magnet to magnetically guide the capsule medical device in a subject. The operation input unit receives operation information to operate magnetic guidance of the capsule medical device. The control device controls the magnetic guidance device to magnetically guide the capsule medical device in response to the operation information input through the operation input unit. The image display device displays a first in-vivo image of the subject imaged by the first imaging unit and a second in-vivo image of the subject imaged by the second imaging unit, and clearly shows which of the first and second in-vivo images is an operation target image at the time of the magnetic guidance of the capsule medical device.