Freemasonry in South Australia and Northern Territory is governed by and under the control of the Grand Lodge of Antient, Free and Accepted Masons of South Australia and Northern Territory Inc.

The Grand Lodge is an association, with membership made up of all Freemasons who are members of constituent lodges and any other Freemason appointed by the Grand Master or elected by Grand Lodge as a member of Grand Lodge. At its head is the Grand Master, who has the right to preside over all meetings, while the overall business is run by or reports to the Board of Management.

Subject to the ample power and authority of the Grand Master, Grand Lodge exercises supreme jurisdiction over the association comprising those Freemasons who are subscribing or honorary members of constituent lodges. The Grand Lodge has sovereign power and is not answerable or responsible to any other Masonic body. The structures, proceedings and management of the Grand Lodge are conducted in accordance with its written Constitutions and Regulations.

The Grand Lodge usually meets for Communication twice each year, in April and in October. An annual Conference is held each October, for discussion of matters of interest to the members of Grand Lodge and of constituent lodges. Each Lodge has one vote. The Conference is a deliberative body. Conference decisions are submitted to the Board of Management of Grand Lodge for consideration and carrying into effect.

Each constituent lodge holds a warrant which was authorised by and continues to be under the control of the Grand Lodge. Constituent lodges must have their Masters installed (whether annually or every 2 years depending on their constitution) by the Grand Master or a Grand Lodge Officer representing the Grand Master. Each lodge has a name and a number, eg Lodge of Friendship No.1 (this lodge was the first to be warranted under the Grand Lodge of South Australia and Northern Territory, hence number 1).

For ease of management, constituent lodges are grouped together into geographical regions known as districts. District Grand Superintendents represent these regions at Grand Lodge as well as representing Grand Lodge within their districts.