National policy for the organization is determined by a governing council consisting of three national officers:
- President (or president-elect or the immediate past president)
Four regional governors and representatives appointed by the
- Mathematical Association of America
- National Council of Teachers of Mathematics
- Society for Industrial and Applied Mathematics
- American Mathematical Association of Two-Year Colleges
The national officers and the governors are elected by chapter sponsors and serve without remuneration. The governing council meets twice a year, in January to set the yearly budget and at the national convention each summer.
The everyday functions of Mu Alpha Theta are handled by the executive director who is appointed by the treasurer with approval of the governing council. The executive director is a non-voting member of the governing council.