Brookhaven is a small city in Lincoln County, Mississippi, United States. The population was 9,861 at the 2000 census. It is the county seat of Lincoln County. It was named after the Town of Brookhaven, New York, by founder Samuel Jayne, in 1818.
According to the United States Census Bureau, Brookhaven has a total area of 7.3 square miles (19.0 km²), of which, 7.3 square miles (19.0 km²) of it is land and 0.04 square miles (0.1 km²) of it (0.27%) is water.
The size of the city was expanded in late 2007 to almost triple the previous size. It was done through a vote of annexation.