In 1989, Heritage Academy was the first school in the Mississippi Association of Independent Schools North Conference to have a black player on its football team. The school received national media attention when two other schools offered to forfeit games rather than play against a racially integrated opponent. The opponents, Sharkey-Issaquena Academy and the East Holmes Academy, claimed that injuries, not race, were the reason for forfeiting the games. Heritage Academy headmaster and head coach Ray Wooten rejected the other schools' denials, referring to them as "a bunch of bull." After seven players and two school board members resigned, East Holmes Academy reconsidered its decision to forfeit. The black player, sophomore running back Scott Fuller, offered to quit the Heritage Academy team so the game could be played, but coach Ray Wooten insisted that Fuller remain on the team. Jabari O. Dunbar was elected the 1st and to date, the only African-American president of Heritage Academy's Student Government Association elected by his peers and the student body in 1991. Jabari then went on to become the 1st African-American to graduate with honors from Heritage Academy in 1992. His sister, Jasa'da Dunbar then became the 2nd African-American to graduate from Heritage Academy in 1998.
Heritage Academy's first athletic director was Billy Brewer. When Brewer later accepted a coaching position at Ole Miss, he told the Clarion-Ledger that his involvement with the all-white academy was his "own business" and that it would not impact Ole Miss's efforts to recruit black players. The Heritage Academy football team won the MPSA AAA championship in 1986 and the MAIS championship in 2012. The Heritage Academy basketball team won MPSA titles in 1992 and 2018. Heritage Academy golf won the MAIS 3A Championship in 2012, 2016, and 2017. In addition to these sports, Heritage Academy also offers baseball, soccer, softball, volleyball, tennis, and track and field. Non-athletic extracurricular opportunities include cheerleading, competitive dance, robotics, quiz bowl, various school clubs, and the spirit store.
