Offices subordinate to Rector
- Rector's Office
- JU Press Office
- JU Legal Team
- Internal Audit
- Protection of Confidential Information and Defence Affairs
- Board of Editors - Alma Mater monthly
- Committee for Jagiellonian University Museum Property
- Office of the Rector's Proxy for Cooperation within the framework of Una Europa
- Office of the Rector's Proxy for Strategic Projects
- Ombudsperson's Office
- Data Protection Inspector's Office
Offices subordinate to Vice-Rector for Medical College
- Department of Human Resources, MC
- Medical College Attorneys
- University Hospitals
- Health and Safety Inspectorate, MC
- Fire Safety, MC
- Personal Data Protetion, MC
- Joint units of JU and MC
- Internal Audit
- Protection of Confidential Information and Defence Affairs
Offices subordinate to Vice-Rector for International Relations
- Office of the Vice-Rector for International Relations
- International Relations Office
- Sports Office
- ZintegrUJ Project Office
- Artistic Ensembles
- 'Responsible Support and Sustainable Development' Project Office
Offices subordinate to Vice-Rector for Educational Affairs
- Office of the Vice-Rector for Educational Affairs
- Centre for Academic Support
- IT Centre
- 'Perfect University - Integrated JU Development' Project Office
Offices subordinate to Vice-Rector for University Development
- Office of the Vice-Rector for University Development
- Office of Institutional Analysis
- Disability Support Service
Offices subordinate to Vice-Rector for Human Resources and Financial Management
- Office of the Vice Rector for Human Resources and Financial Management
- Human Resources
- Public Procurement Office
Offices subordinate to Vice-Rector for Research
Offices subordinate to Chancellor
- Chancellor's Office
- Department of Operations
- Centre for Communications and Marketing
- Staff Assistance Fund
- Rector's Guard
- Security and Safety
- Student Centre for Support and Adaptation
- Deparment of Security, Safety and Equal Treatment
Offices subordinate to Deputy Chancellor for General Affairs
- Office of the Deputy Chancellor for General Affairs
- Office of Inventory Management
- Department of Supply
- Health and Safety Inspectorate
- Fire Safety Inspectorate
Offices subordinate to Deputy Chancellor for Real Estate Management
- Office of the Deputy Chancellor for Real Estate Management
- Administration Office for the Campus of the 600th Anniversary of the JU Revival
- Office of Real Estate Management
Offices subordinate to Deputy Chancellor for Technology and Investments
- Office of the Deputy Chancellor for Technology and Investments
- Department of Maintenance
- Department of Construction Projects
- Department of Renovation
- Telecommunications
Offices subordinate to Deputy Chancellor for Medical College
- MC Department of Operations and Marketing
- MC Department of Public Procurement
- MC IT Centre
- MC Department of Supply
- MC Department of Resources Management
- MC Department of Construction, Renovation and Maintenance
Offices subordinate to Bursar
- Bursar's Office
- Analysis and Reporting Manager
- Manager of Procedure Optimisation
- Department of Budget, Control and Analysis
- Tax Unit
Offices subordinate to Deputy Bursar for Finances
Offices subordinate to Deputy Bursar for Accounting
- Department of Property Records
- Department of Accounting
- Department of Domestic Projects Financial Management