The Town of Henderson is in the west part of the county and is southwest of Watertown.
This area had long been occupied by the Onondaga people, a nation of the Iroquois Confederacy, a Native American coalition of tribes who controlled most of upstate and western New York around the Great Lakes by the 15th century. Because most nations of the Iroquois Confederacy had allied with the British in the American Revolutionary War, after the latter's defeat, the United States forced the Iroquois to cede most of their land in New York under the terms of the peace treaty. The tribes moved to Canada, where the British offered them land in what is now Ontario.
New York made available for sale millions of acres of the former Iroquois lands at very low prices in an effort to stimulate settlement and agricultural development of its western and upstate territories. It offered some land to veterans as payment for their service during the war. Speculators based in New York City bought huge portions of land and sold them later for development.
As a result, by 1801 the town had been surveyed and divided into lots, but settlers did not begin to arrive until 1802. Most settlers migrated from New England, which had limited lands available for farming. The Town was officially organized in 1806 from territory previously part of the Town of Ellisburg.