It is an object of the present invention to provide a destination estimating system and a destination estimating method capable of estimating a destination with a high degree of accuracy even when a user uses a detour or stops off somewhere. The destination estimating system of the present invention includes: obtaining a traveling area and a traveling link of a moving body; obtaining, as a traveling history, an area history for storing, for each area, information of a past destination to which the moving body has traveled via the area previously and a link history for storing, for each link, information of a past destination to which the moving body has traveled via the link previously; estimating, based on the traveling area and the area history, a value regarding a probability of traveling to the past destination as an area estimation value; estimating, based on the traveling link and the link history, a value regarding a probability of traveling to the past destination as a link estimation value; and estimating the destination from the past destination based on the area estimation value and the link estimation value.