The school opened in 1998 at the site of the Charlotte Islamic Center.

[1] After the September 11, 2001 attacks the school received threatening phone calls, forcing it to close for a week.

[2] In 2004, the school moved to a building owned by a local Presbyterian church after disagreements with the Islamic Center over control of religious education.

[3] There was some controversy amongst Presbyterians when Christian symbols were removed or covered, with the permission of the church.

[4] After the re-merger, the board of the new school changed its name to Charlotte Islamic Academy.