Brookhaven is a small city in Lincoln County, Mississippi, United States, 55 miles south of the state capital of Jackson. The population was 11,67…Brookhaven is a small city in Lincoln County, Mississippi, United States, 55 miles south of the state capital of Jackson. The population was 11,674 people at the 2020 U.S. 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.