Marathon is within the bounds of the former Central New York Military Tract. The first settlers entered the town in 1794.
The town was formed from part of the Town of Cincinnatus as the "Town of Harrison" in 1818. The name was changed to "Marathon" in 1828 because another town in New York was named Harrison.
The Village of Marathon set itself off from the town in 1861 by incorporation.
Thurlow Weed, political boss and publisher, came to this town with his family in 1808.