The National MagLab is a large institution jointly operated for the National Science Foundation by Florida State University, the University of Florida and Los Alamos National Laboratory (with sites at each of those locations) under a cooperative agreement that establishes the lab's goals and objectives.

The lab's scientific direction is overseen by the Science Council, In addition, two external committees, the Users Committee and the External Advisory Committee, provide advice on issues critical to the successful management of the lab.

The lab’s leadership team works collaboratively to support and advance the scientific mission of the National MagLab.

Made up of representatives from academia, government and industry, this committee offers advice on matters critical to the successful management of the lab.

The Science Council helps set the lab's scientific agenda and serves as an internal advisory group on global scientific issues and potential opportunities for the laboratory.