The rectorate comprises the following sections and subdivisions:
- Rector's Office
- Department of Legal Affairs
- Department of Internal Auditing
- Academic Senate Office of CTU
- Department of PR and Marketing
- Department of Development
- Department for Education and Student Affairs
- Centre for Information and Counselling Services (CIPS)
- Support Centre for Students with Special Needs (ELSA)
- Department of Science and Research
- Department of Technology Transfer
- Technology Transfer Office
- Patent Centre
- Department of Structural Funds
- International Office
- Department for Quality and the Information System
- Department of Construction and Investment
- Bursar's Office
- Department of Financial Management and Controlling
- Department of Budgeting and Finances
- Budgeting Office
- Financial Office
- Employee Office
- Department of Property Management
- Facility Management Office
- Transportation Office
- CTU Archive
- Department of Archive Management and Research Department
- Archive Services
- Department of Records Management
- Facility Management of Jugoslávských partyzánů Building