Eliot was originally part of the Piscataqua Plantation. It later became a part of the township of Kittery, and was known as the Upper Parish. In 1810 Eliot separated from Kittery to become it's own town.

Eliot is known for several historic points including it's former days as a shipyard and was the site of the earliest power mill in Maine. The historical buildings of today's Eliot include the William Fogg Library, the William Fogg House, the Dr. Willis Homestead (1725), the Libby Home (1768 - a former roadside tavern). The site of the First Quaker Meeting House (1776) and the old Kittery House (1638).