Brookhaven Academy (BA) is an independent, co-educational college preparatory school in Lincoln County, Mississippi, near Brookhaven. The school was founded in 1970 as a segregation academy.

In January 1970, the Fifth U.S. Circuit Court of Appeals ordered Mississippi to desegregate its public schools. Brookhaven Academy, Inc. was founded in 1970 as a segregation academy.

The IRS did not confer non-profit status to Brookhaven Academy Educational Foundation until 1983. In 1988, Black students walked out of nearby Brookhaven High School in protest when that school hired a coach from Brookhaven Academy, which was considered a grievous racial provocation. During the 2015-16 school year, Brookhaven Academy enrolled a single black child. In 2018, the school received attention when it was revealed that U.S. senatorial candidate Cindy Hyde-Smith sent her daughter to this school.

Racial distribution in 2015-16

Surrounding Lincoln County was about 30% Black.

Racial distribution in 2017-2018

Surrounding Lincoln County was about 82% white, 16% Black, and 2% Hispanic.

Brookhaven plays football in the MAIS 4A league.