ISASA’s General Council, which includes its office-bearers and delegates from its five regions, determines the Association's policy. The Executive Committee expedites policy decisions of the Council. Each region also has a Regional Committee, as well as a Chair and a Regional Director.

When ISASA was established in 1999, the heads' and the bursars' associations changed their names and constitutions to become constituent members of ISASA, as the Southern African Heads of Independent Schools Association (SAHISA) and the Southern African Bursars of Independent Schools Association (SABISA) respectively.

Prior to 2001, a national consultative body for all the independent school associations, known as the National Joint Liaison Committee (JLC) existed. At the end of 2000, the JLC drew up a constitution to cement the good working relationships between these associations and to facilitate interaction with government. The new body is known as the National Alliance of Independent School Associations of Southern Africa (NAISA).