The first segregation academies were created in the late 1950s as a result of the U.S. Supreme Court ruling Brown v. Board of Education, which required public school boards to eliminate segregation "with all deliberate speed." Because the ruling did not apply to private schools, the creation of segregation academies was a way to keep segregation intact. Private academies operated outside the scope of the Brown v. Board of Education ruling and could therefore effectively maintain racial segregation. While there is some debate about why whites pulled their children out of public schools (with whites insisting that "quality fueled their exodus" while blacks say "white parents refused to allow their children to be schooled alongside blacks") there is no debate that many white children were pulled out of region's public schools and instead educated in private schools. Across the nation it is estimated that at least half a million students were withdrawn from public schools between 1964 and 1975 to avoid mandatory desegregation. As Archie Douglas, the headmaster of the Montgomery Academy (a school reputed to have been founded in response to desegregation) has said, he is sure "that those who resented the civil rights movement or sought to get away from it took refuge in the academy."
As a result of the creation of segregation academies, a number of Southern schools were identified by name in Allen v. Wright, a lawsuit by black parents in seven U.S. states. The parents sued the Internal Revenue Service, contending that IRS guidelines for determining whether a private school was racially discriminatory were insufficient. The case was decided in 1984 by the U.S. Supreme Court, which ruled that citizens do not have standing to sue a federal government agency based on the influence that the agency's determinations might have on third parties (such as private schools). The judges also noted the parents were in the posture of disappointed observers of the governmental process, that although the complaint asserted that "there are more than 3,500 racially segregated private academies operating in the country having a total enrollment of more than 750,000 children" (J.A. 24), it cited by name only 19 "representative" private schools, and that the parents did not allege that they or their children had applied to, been discouraged from applying to, or been denied admission to any private school or schools.
Despite this victory, as social patterns in the United States changed many segregation academies either opened their doors to students of all races or had their nonprofit status revoked by the IRS.
A large number of Christian schools in the United States reportedly began as segregation academies.
In Mississippi, many of the segregation academies were first introduced in the Mississippi Delta region in the northwestern part of the state. The Delta has historically had a very large Black population and the threat of integration prompted segregation academies to be created in every county in the Delta. These academies are still in operation in places from Indianola (home of the original White Citizens Council chapter) to Humphreys County (site of the murder of Reverend George Lee of Belzoni and elsewhere. These schools have nominally integrated now, however, and have a few Black students just as the public schools of the Delta overwhelmingly have only a few non-Black students.
In Virginia, segregation academies were part of a policy of massive resistance declared by U.S. Senator Harry F. Byrd, Sr., to unite other white Virginian politicians and leaders in taking action to prevent school desegregation after the Brown v. Board of Education Supreme Court decision in 1954.
In 1956, the Virginia General Assembly passed a series of laws to implement massive resistance. One of these laws created a program of "tuition grants" which could be given to students so they could attend a private school of their choice. In practice, this meant support of all-white schools that appeared as a response to forced integration, and these newly formed schools became known as the "segregation academies."
When faced with an order to integrate, Prince Edward County closed its entire school system in September 1959 rather than integrate. The county kept its entire school system closed until 1964. Many white students were able to get educated at the newly-created Prince Edward Academy, which operated as the de facto school system, enrolling K-12 students at a number of facilities throughout the county. Even after the re-opening of the public schools, the Academy remained segregated, losing its tax-exempt status in 1978.
Although on January 19, 1959, the Virginia Supreme Court of Appeals struck down the linchpin of the Massive Resistance laws, the one closing schools about to be integrated, individual state tuition grants to parents allowed them to fund the segregation academies. It was not until 1964 that the U.S. Supreme Court outlawed Virginia's tuition grants to private education where the public schools had been closed, such as in Prince Edward County. This decision was effectively the end of the Massive Resistance movement within the state government, and it dealt the segregation academies a fatal blow. Other later rulings put their tax exemption status in jeopardy if they practiced racial discrimination.
In 1986, Prince Edward Academy accepted black students. Today it is known as the Fuqua School. All of the other segregation academies either closed or adopted non-racial discrimination policies. One, Huguenot Academy, merged with Blessed Sacrament High School, a nearby Catholic High School, to become Blessed Sacrament-Huguenot.