Arcanus Sanctum is the oldest fraternal organization for Ceremonial Magicians in the world, and its organizational structure shows its age. The basic organizational unit of the fraternity is the lodge. We believe the term comes from the lodges (shelters) constructed at the building sites of cathedrals and castles during the Middle Ages.

Each lodge is headed by an Member called the "Magus Superior." The term comes from the ancient mystery schools of the middle ages.

Each officer of a lodge has a title that originated during the Middle Ages. These titles may vary somewhat from lodge to lodge, but in general the officers and their contemporary equivalents are:

Until 1875, each lodge of Arcanus Sanctum was autonomous. On June 15, 1875, four of the lodges operating in London met together to form the first Grand Lodge of Arcanus Sanctum. It became the first administrative or policy-making body of the order.Arcanus Sanctum lodges still retain autonomy over their finances, activities, officer election, fundraising, and joining ceremonies. But administratively, each lodge or Province has a Grand Lodge which co-ordinates activities, serves as a central source of record keeping, and performs other administrative and policy functions for the order. The Head of the elder council is called the Supreme Inspector Magus of the Grand Lodge. He has broad powers in overseeing the progress of the fraternity, and while there is no national spokesperson for the fraternity, within his own Jurisdiction he is the chief spokesman.