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SFedU is managed in accordance with the Law of the Russian Federation, regulations of higher education and the University Charter.

Charter (as well as its changes and additions) is adopted by joint meeting (conference) of the University teaching and research staff and other representatives of personnel and students.

The elected structure unit - Academic Council provides general academic governance of the University. The Academic Council involves rector, who heads the Council, vice-rectors. Other members of the Council are elected at the joint meeting (conference) by a secret vote.

Structure, power, election system and activities of the Academic Council are identified by the University Charter.

Rector of SFedU acts as the highest executive officer. He is approved for the position by the federal executive body. Rector appoints vice-rectors and directors of main structural units - SFedU institutes.

Rector annually reports at the extended Academic Council meeting with the participation of the teaching staff, researchers and other categories of employees, employers and community. Rector issues orders, instructions and other documents of compulsory implementation for staff and students in accordance with his limit of authority.  Rector has a right to:

- Identify in accordance with the RF Law employment duties of the University staff;
- Represent the University interests in relations with organizations of different forms of property and citizens;
- Approve regulations on structural units;
- Administer the University funds in accordance with regulations;
- Perform personnel policy;
- Organize the University and its structural units work;
- Exercise power in accordance with the reserved with law and personal contract rights.

Some part of Rectors decision authority can be delivered to vice-rectors and other leading university managers. Allocation of responsibilities between vice-rectors is set by rectors order and is disseminated within all university staff. The number of vice-rectors is identified by rector according to university development goals.

General governance of the main structural units (institutes) is done by their Academic Councils. Their formation procedure and work are settled by special Regulations approved by rector. Director of institute acts on by virtue of the power of attorney as an immediate executive officer.

Academies, Faculties and SFedU Institutes are governed by their Academic Councils. Their formation and work is settled by Regulations on faculty approved by the University Academic Council.  Dean of the faculty heads the Faculty Academic Council and acts as a main manager. Dean is responsible for all faculty activities before rector and academic council.

Department is the main university academic-research unit with laboratories, scientific-research groups. Department work is regulated by the Instruction approved by the University rector. It makes own decisions on organization of training and research process, initiates preparation of materials to conclude agreements for specialists training, conduction of research, rendering of additional services. Department is headed by Department Chairman, a highly qualified specialist holding academic degree.

Students take part in the University governance through representational structures - university and faculty Academic Councils, community, Student union working in accordance with the legislation of the Russian Federation.