[1][8][9] It was named for Cape Fear Military Academy, an independent school for boys in Wilmington that operated from 1868 until 1916.

In 1967, the civil rights activist Lee Shelton claimed that Ku Klux Klan was raising funds to establish Cape Fear Academy as a private school for white students.

[23][24][25] The lawsuit led to renewed media attention concerning Cape Fear Academy's history of racial and gender discrimination.

[29] In 2022, the school purchased an 11-acre (4.5 ha) plot of land originally owned by Trinity United Methodist Church.

Cape Fear Academy offers affordability plans for tuition; a majority of the awards go to students in the Middle and Upper School.

[35] The Upper School has a student-government association with a branch called the Honor Council that deals with and makes recommendations for disciplinary infractions.