[2] The county is named after James Madison,[3] the fourth president of the United States, and was first formed in 1806.

The historic Oneida Indian Nation is an Iroquoian-speaking people who emerged as a culture in this area about the fourteenth century and dominated the territory.

In the years prior to the outbreak of revolution in 1776, tensions rose in the frontier areas upstate and most of the Loyalists in Tryon County fled to Canada.

In 1784, following the peace treaty that ended the American Revolutionary War, New York changed the name of Tryon County to Montgomery County, in honor of the general, Richard Montgomery, who had captured several places in Canada and died attempting to capture the city of Quebec.

In the postwar treaty, the four Iroquois nations who had been allies of the British were forced to cede their lands; most of their peoples had already migrated to Canada to escape the worst of the fighting on the frontier after Sullivan's Raid.

This was later divided to form the present Allegany, Cattaraugus, Chautauqua, Erie, Genesee, Livingston, Monroe, Niagara, Orleans, Steuben, Wyoming, Yates, and part of Schuyler and Wayne counties.

The two peoples were pressured to leave New York for Wisconsin in the 1820s, to make more land available for European-American settlement.

In the late twentieth century, the three recognized Oneida tribes: of Wisconsin, New York, and the Thames reserve in Canada, filed suit in a land claim against New York for its treaty and forced purchase of their ancestral lands after the American Revolutionary War, seeking the return of thousands of acres.

Several private and public interests oppose the deal, including other federally recognized tribes in New York.

Madison County contains the geographic center of the state at Pratts Hollow in the Town of Eaton.

The Great Swamp, formerly located south of the lake, was a rich wetlands habitat important to many species of birds and wildlife.

This was drained by local and state construction projects in the early decades of the twentieth century, chiefly by Italian immigrants.

The fertile soil supported high production of onions and other commodity crops, and the Italian families grew wealthy from their work.

Oneida Lake is the northern border with part of Oswego County on the opposite shore.

Hispanic or Latino people of any race were 1.06% of the population; 16.1% were of German, 15.6% English, 15.5% Irish, 12.1% Italian, and 8.0% American ancestry according to Census 2000.

The one exception to this was in 1964, as the county swung strongly to the Democratic column for the first time thanks to Barry Goldwater's conservatism alienating the Northeast, giving Lyndon B. Johnson a wide margin of victory as he won every county in the state and won by a landslide nationally.