The Faculty has its organizational units aimed at enhancing the system and harmonizing activities of the Faculty, as well as addressing the issues of common interest for implementation of the scientific, teaching and higher-education work. The organizational units of the Faculty are departments, laboratories, administration and institutes. Along with the Faculty employees, persons from other faculties, part time associates and scientists can also participate in the work of organizational units.

Departments and laboratories are the Faculty's organizational units involved in the realization of university study programmes and perform scientific, teaching and highly qualified work.
The following departments operate at the Faculty of Civil Engineering University of Mostar:
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• Department of Mechanics, Materials and Structures (Head Mladen Glibić, Ph.D.)

• Department of Hydraulic Engineering and Geotechnics (Head Zoran Milašinović, Ph.D.)

• Department of Roads and Construction Management (Head Ivan Lovrić, Ph.D.)

Department of Architecture and Urban Planning (Head Valerija Kopilaš, Ph.D.)