A navigation system includes an alignment unit configured to generate corrected position information in which position information of a viewpoint of an endoscope that is inserted in a subject is aligned with a three-dimensional image of a luminal organ, a determination unit configured to determine performance/non-performance of observation of a branch conduit based on the corrected position information, a target setting unit configured to set one unobserved conduit as a first target region based on a distance between the position information of the current viewpoint and the unobserved conduit, and a navigation information generation unit configured to generate navigation information for the first target region.