The dean is at the head of the faculty.

Faculty Management:

• dean

 Vice-deans
    - for Internal Affairs and Development
    - for Education
    - for Research Activity
    - for External Relations

• Executive secretary

The dean’s office is formed by the sections as follows:

• Study department
• Section of Research Activity
• Section of Internal Affairs and Development
• Section of External Relations

Departments:

•  Department of Transport Management, Marketing and Logistics
•  Department of Transport Technology and Control
•  Department of Informatics in Transport
•  Department of Transport Means
•  Department of Transport Infrastructure
•  Department of Mechanics, Materials and Machine Parts
•  Department of electrical and electronic Engineering and Signaling in Transport

Detached branches:

•  Jan Perner Transport Faculty Detached Branch in Česká Třebová
•  Educational and Informational Branch of Jan Perner Transport Faculty in Prague

Other workplaces:

•  DFJP Accredited Laboratory (abbrev. AL)
•  Department of Traffic Accident Analysis DFJP (abbrev. ÚADN) 
•  Research Centre of Railway Vehicles (abbrev. VCKV)
• Transportation Laboratory Jan Perner Transport Faculty (abbrev. PL)