In 1668, Chief Captain Wesumbe of the Newichawannock Abenaki tribe deeded Francis Small, a trader from Kittery, the Ossipee Tract. This included Cornish, Parsonsfield, Newfield, Limerick, Limington and Shapleigh. Francis Small then sold a half interest to Major Nicholas Shapleigh of Eliot. In 1770, the unrecorded deed was discovered and Shapleigh's heirs took Parsonsfield, Shapleigh and one half of Limerick.

First called Hubbardstown, it was settled in 1772 when Simeon Emery erected a sawmill at the foot of Mousam Pond. On March 5, 1785, the town was incorporated as Shapleigh, named for its early proprietor. In 1830, Shapleigh's west half was set off and incorporated as Acton. In 1846, a portion of Shapleigh was annexed by Newfield. Shapleigh annexed an eastern portion of land from Waterboro in 1854.

There were sawmills in Emery Mills, Shapleigh Corner and North Shapleigh, which also had a woolen textile factory and leather board factory. For a few years beginning in 1837, iron was produced at a blast furnace in North Shapleigh from bog iron retrieved from Little Ossipee Pond. Foundations, walls, and slag remained at the site at the time of a 2003 Maine Geological Survey publication on the site.