The Order of the Arrow has three distinct organizational levels: lodges, sections, and regions. Lodges carry out the Order of the Arrow program at the local level and are closely tied with BSA councils. Sections consist of several lodges within a geographic region and regions in turn consist of sections within a geographic region of the United States. Lodges, sections, and regions each have a distinct set of responsibilities which ensure that the OA program runs smoothly.

Each section is led by a chief, vice chief, and secretary, who play a crucial part in making the annual Conclave a success. The section leads training seminars, promotes national programs of emphasis, and provides resources to local lodges. The section chief presides over the Council of Chiefs, attended by delegates of each member lodge.