Each of the eight RSPCA Australian member Societies operate independently, however, the National Council of the RSPCA meets three times a year to formulate new national policy, plan future directions of the RSPCA and to offer advice to government and industry on national animal welfare issues. The sixteen member National Council is made up of two members (a President and Chief Executive Officer) from each state and territory Society.

Each state and territory Society is governed by a Council of volunteers who are drawn from the community. Each council has an elected President. The core of administration, 'hands-on' and inspectorial work of the RSPCA Societies is carried out by paid staff, usually under the management of a Chief Executive Officer. Volunteers also work 'hands-on' with RSPCA Societies.

All new policies require the unanimous vote of the National Council before it is accepted as Policy.