Before European settlement, the land that comprises Flemington was the territory of the Lenni Lenape Native Americans, as was all of Hunterdon County. In 1712, as part of a land parcel of 9,170 acres (37.1 km2), the Flemington area was acquired by William Penn and Daniel Coxe.
The surrounding fertile farmland dictated that the beginnings of Flemington should be essentially agricultural. Early German and English settlers engaged in industries dependent on farm products. As time passed poultry and dairy farms superseded crops in agricultural importance. An example of early settlement families was Johann David and Anna Maria Ephland, who immigrated in 1709 from Germany through London to New York and settled on his 147.5-acre (0.597 km2) farm in 1710. They raised their seven children, and two from his previous marriage, on the farm that now makes up the core of Flemington.
In 1785, Flemington was chosen as the County Seat of Hunterdon. Fire destroyed the old courthouse in 1826 and the City of Lambertville made an attempt to have the Seat moved, to no avail. Flemington remained the County Seat and the Courthouse which stands today on Main Street was built.
What is now Flemington was originally formed as a town by an Act of the New Jersey Legislature on March 14, 1870, within portions of Raritan Township. It became a village as of June 11, 1894, still within Raritan Township. Flemington was finally incorporated as an independent borough by an Act of the New Jersey Legislature on April 7, 1910, based on the results of a referendum held on April 26, 1910, and was formally separated from Raritan Township. The borough’s incorporation was confirmed on April 27, 1931.