Offices and officers subordinate to Rector
- Rector's Office
- JU Press Office
- Office of Rector's Proxy for Internationalisation
- JU Legal Team
- Internal Audit
- Protection of Confidential Information and Defence Affair
- Rector's Consultant for Investment and Modernisation of the Campus of the 600th Anniversary of the JU Revival
- Board of Editors - Alma Mater monthly
- Office of Institutional Analysis
- Strategy Implementation Monitoring
- Committee for Jagiellonian University Museum Property
Offices subordinate to Vice-Rector for Human Resources and Financial Management
- Office of the Vice Rector for Human Resources and Financial Management
- Office of Human Resources
- Staff Benefits Office
- Internal Control
- JU Academic Choir Camerata Jagellonica
- Słowianki Song and Dance Ensemble
Offices subordinate to Vice-Rector for University Development
- Office of the Vice-Rector for University Development
- Public Procurement Office
- Disability Support Service
- Strategic Analyses
- Sports Office
- ZintegrUJ Project Office
Offices subordinate to Vice-Rector for Research and Structural Funds
- Office of the Vice-Rector for Research and Structural Funds
- International Relations Office
- Centre for Project Administrative Support
Offices and officers subordinate to Vice-Rector for Educational Affairs
- Office of the Vice-Rector for Educational Affairs
- Centre for Academic Support
- Computer Network Department
- Office of IT Services
- University Website
- 'Perfect University - Integrated JU Development' Project Office
Offices and Officers subordinate to Vice-Rector for Medical College
- Office of the Vice-Rector for Medical College
- Teaching and Academic Careers, MC
- Department of Project Administrative Support and Structural Funds, MC
- Clinical Office, MC
- Department of Human Resources, MC
- Medical College Attorneys
- "New University Hospital in Kraków-Prokocim" Project Office
- University Hospitals
- Joint units of JU and MC
Offices and officers subordinate to Chancellor
- Chancellor's Office
- Office of Inventory Management
- Department of Operations
- Centre for Communications and Marketing
- Department of Supply
- Staff Assistance Fund
- Rector's Guard
- Security and Safety
Offices and officers 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 and officers 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 and officers subordinate to Deputy Chancellor for Medical College
- MC Office of Operations and Marketing
- MC Office of Public Procurement
- MC IT Centre
- MC Department of Supply
- MC Department of Resources Management
- MC Department of Construction, Renovation and Maintenance
Offices and officers subordinate to Bursar
- Bursar's Office
- Analysis and Reporting Manager
- Manager of Procedure Optimisation
- Department of Budget, Control and Analysis
- Tax Unit
Offices and officers subordinate to Deputy Bursar for Finances
Offices and officers subordinate to Deputy Bursar for Accounting
- Department of Property Records
- Department of Accounting
- Department of Domestic Projects Financial Management