Henderson is a town in Jefferson County, New York, United States. The population was 1,360 at the 2010 census. The town is named after William Henderson, the original land owner.
The Town of Henderson is in the west part of the county and is southwest of Watertown.
The town had been surveyed and divided into lots by 1801, but settlers did not begin to arrive until 1802. The town was established in 1806 from the Town of Ellisburg.