Although it had been thought that the first permanent white settler in the area was John Thompson, further research has shown that Abraham A. Cuddeback from Minisink, New York was the first to arrive in 1794.

The old Genesee Road, which connected Utica, Marcellus, Auburn, Geneva and Avon became the Seneca Turnpike in 1800; the first bridge across Skaneateles Creek was built that year.

It may be the work of Ithiel Town, the partner of Alexander Jackson Davis, who designed the house of Reuel Smith, a wealthy Massachusetts importer who retired to Skaneateles.

Built in 1852, the architecturally distinguished house, designed in the Gothic Revival style, has been listed in the National Registry; its plans are in the Library of Congress.

Fuller and his wife Lydia maintained an active Underground Railroad station at their village home (built 1815, extant at 98 Genesee Street.)

Fuller was co-founder of the British-American Institute, a Canadian school for fugitive slaves, together with the adjoining settlement of Dawn near Dresden, Ontario.

The Village of Skaneateles is governed by a five-person board consisting of the mayor and four trustees, each of whom is elected to a two-year term.

[7] On April 1, 2021, Mary Sennett succeeded Marty Hubbard as mayor, the first time a female has held this office in village history.

[10] The Town and Village Joint Comprehensive Plan of 2005 examined consolidating the two entities into one government to reduce redundancies and create efficiencies.

[11][12] In 2009, the New York State Legislature passed legislation to ease such consolidations under the premise that they would create efficiencies and reduce tax burdens.

[13] The village consists of a small commercial core with surrounding residential streets; the downtown area sits immediately on the lake.

Village attractions include boat excursions, inns, restaurants and a spa, as well as boutique shopping and art galleries.