The Order consists of fraternities at multiple levels: local, regional, national, and international. Each level is governed by a Council. Members of each level's Council are elected by those from the level immediately below it. The local Council is elected by professed members of the Order who are members of that fraternity.

Each level's Council also has an appointed Spiritual Assistant, whose role is to ensure the fidelity of the fraternity to the Franciscan charism. In this manner the Franciscan First Orders and Third Order Regular form a strong bond with each fraternity.

The governing documents of the Secular Franciscan Order are its Rule, the General Constitutions, the International Statutes, and the National Statutes. There are also numerous policies promulgated by the National Executive Council and Council of National Spiritual Assistants. Additionally, each Region may issue its own set of Guidelines to govern its specific needs.

The Rule of the Secular Franciscan Order was approved in 1978 and describes the structure and origin of the Order, how members should live, and the life of a fraternity. It can be found in English and Spanish, as well as other languages on the OFS-USA web site. These are updated translations (2020); for more information see the OFS-USA website.

The General Constitutions govern the entire worldwide Order. They were last revised in 2000. A more detailed description can be found on the OFS-USA website. A copy can be found on the OFS-USA website in both English and Spanish, and other languages.

The International Statutes are based on the Rule and General Constitutions. They were last revised in 2024, and an English translation can be found on the CIOFS website.

The National Statutes are specific to the USA and address matters in greater detail. They were last revised in 2010. Another revision is currently in progress. These statutes must be consistent with all higher documents.

There is also a set of National Guidelines on a variety of topics. These were created and promulgated by joint effort of the National executive Council (NEC) and the Conference of National Spiritual assistants (CNSA). TO view them, visit the Governing Documents page of the OFS-USA website, click the "+" to the left of the words National Guidelines, and a list of them will appear.