The area was ruled by Great Britain as part of the Province of Quebec and then acquired by the United States.

Winneconne's European-American settlement began in the mid-19th century with Yankees who migrated from New England and the Northern Tier, added to by waves of immigrants: Irish, Germans, and Norwegians.

Originally, Winneconne had many different spellings: Winneconnah, Winnekonah, Wau-nau-ko, and Winnikning, which were transliterations from the Menominee and other Indian names for the site.

In 1851 the recently constituted village board officially settled the spelling of the name as Winneconne.

Chief Oshkosh negotiated with the President to keep other lands in this area, as more than 2500 of his people refused to move to Minnesota, as was desired by the federal government.

Rush built a float bridge, and set up toll stations to recover his costs.

In Winneconne's early years, mills were built along the river as the first industries, to process lumber, grain, and operate tanneries.

The many shipyards built and repaired fleets then made up primarily of wooden boats and ships.

The Wolf River Bridge, carrying WIS 116, was built in 1934 during the Great Depression with support from the federal government, under President Franklin D. Roosevelt's WPA projects for investment in infrastructure.

[8] This non-redundant bascule bridge is now functionally obsolete because of its narrow deck width and aging materials.

As it is very important to the Main Street of the village, and connections to other cities in the region, the state has approved a new bridge to carry WIS 116.

[9] In 1967, as a result of the town name being inadvertently left off the official Wisconsin road map, a secret committee led by Vera Wentzel-Kitchen of the Arrowhead Restaurant formulated a plan to secede from Wisconsin, set up toll gates on local roads, and begin annexation of nearby communities, starting with the city of Oshkosh, to form a Sovereign State of Winneconne.

The secession was not recognized by any formal government and was merely a gesture indicative of the village's displeasure with state officials.

An annual Sovereign State Days celebration commemorates the event, and a logo showing poison ivy, a skunk, a sheepshead, and a dodo bird is displayed throughout the town.

Many bass fishing tournaments are based in Winneconne due to its central location on the chain.

The library has 35,000 holdings, approximately 30,000 of which are books and the balance consisting of video, audio, and other materials in electronic format.