A ship reverse-run detection system includes a memory, and a processor coupled to the memory, wherein the processor is configured to: detect a direction of change in a position of a ship based on position information of the ship which is detected by a position detection device which is mounted on the ship, specify a traveling direction associated with a navigation region of the ship which is specified based on the position information, by referring to a storage which stores the navigation region and the traveling direction in association with each other, and detect reverse run of the ship in the navigation region based on the magnitude of an angle between the direction of the change and the traveling direction.