The area around present-day Flemington was first settled by families of the Midway District in 1815, seeking retreat from their swampy rice plantations on the coast. William Fleming was the most prominent of these men, establishing a retreat known as Gravel Hill. To ensure a sense of community, Fleming gave lots to his friends, including John Osgood, Oliver Stevens, Peter Early Winn, Major John Bacon, and Joseph Norman.

By the early 1830s, a church at Gravel Hill was established, and served as a branch of Midway Congregational Church. In 1850, the retreat had grown enough to warrant a more proper name, and citizens chose the name Flemington, in honor of William Fleming. Soon thereafter, in 1852, congregants and enslaved carpenters built the community landmark which became Flemington Presbyterian Church after the Civil War.

Flemington was officially chartered in 1941. This Craftsman-style bungalow, which served for many years as the manse of the Presbyterian Church, became the city hall in 2005.