St. Cloud State University is organized into five autonomous colleges and schools with two schools embedded in each of the colleges.
The following individuals and units report directly to the Provost and Vice President for Academic Affairs.
| Associate Provost for Academic and Faculty Affairs | Ajay Panicker |
| Associate Provost for Institutional Effectiveness and Academic Quality | Michele Mumm |
| Associate Vice President for Academic Operations and Resources | Brandon Johnson |
| University Curriculum Coordinator | Bill Cook |
| College of Education and Learning Design | King Banaian, Interim Dean |
| College of Health and Wellness Professions | Roxanne Wilson, Interim Dean |
| College of Liberal Arts | Raymond Philippot, Interim Dean |
| School of the Arts | Melissa Krause, Interim Associate Dean |
| College of Science and Engineering | Adel Ali, Dean |
| School of Computing, Engineering, and Environment | Maureen Tubbiola, Associate Dean |
| Herberger Business School | Katherina Pattit, Dean |
| Honors College | Jennifer Cavalli, Executive Director |
| School of Graduate Studies | Claudia Tomany, Associate Provost for Research and Sponsored Programs and Dean of Graduate Studies |
| University College | Feng-Ling Johnson, Associate Vice President for Student Success and Dean of University College |
| Center for Continuing Studies | |
| Center for Excellence in Teaching and Learning | Janet Tilstra, Director |
| Center for Holocaust and Genocide Education | Emil Towner, Director |
| Center for International Studies | Shahzad Ahmad, Associate Vice President |
| Office of Research and Sponsored Programs | Claudia Tomany, Associate Provost for Research and Sponsored Programs and Dean of Graduate Studies |
| SCSU Online |
David Blanchard, Director of SCSU Online and Distance Learning |
| University Library | Rhonda Huisman, Dean |