The leadership structure of Rainbow begins with each local Assembly and extends to the State (Grand) and International (Supreme) Assembly levels. Each local Assembly is made up of five line officers (Rainbow girls who lead the Assembly under the direction of a Mother Advisor and an adult Advisory Board) plus 13 appointed officers. The adult governing body of each Rainbow Assembly is known as the Advisory Board and is comprised of 7-15 adults, who are either parents, grandparents or legal guardians of Rainbow girls, or who are affiliated with and in good standing with various other Masonic fraternal organizations, including Masons, Eastern Star and Amaranth. These adults volunteer their time.

The subordinate assemblies (local groups) are directed under the state Grand Assemblies and the state is under the International Supreme Assembly. Each Assembly has its own set of officers and a Mother Advisor, who is what her title implies, an advisor to the girls. In the state organizations, they prefix “Grand” to the title, and in the International, it is the “Supreme” body. Each Rainbow Assembly is organized and governed by a uniform code of bylaws set forth by Supreme Assembly, headquartered in McAlester, Oklahoma.

In the local Assembly, the Advisory Board composed of Masons, Eastern Star and Amaranth members, and Rainbow Parents, who stand back of the Assembly to guide and direct the girls. In the state organizations, called Grand Assemblies, there is a State Executive Committee. The International group over all of them is called the Supreme Assembly. Each state has an outstanding Eastern Star or Masonic Brother in Charge. They are known as Supreme Inspectors or Supreme Deputies, who report all activities in their various states to the International Supreme Office.