The Town of Cincinnatus is in the eastern part of the county and is east of the City of Cortland.
The region was part of the Central New York Military Tract used to pay soldiers of the American Revolution. One of the townships was named Cincinnatus. Members of the Oneida tribe persisted in the town during its early history.
The town was first settled around 1795. It was one of the original six towns of Cortland County. The town was formed from the Town of Solon in 1804. In 1818, Cincinnatus was split so that part of its territory was used to create the Towns of Freetown, Willet, and Marathon.