The Faculty of Civil Engineering and Architecture was established in 1982. Apart from a three-year undergraduate study programme (Civil Engineering and Arhitecture) and two-year graduate study programmes (Hydraulic Engineering, Load-Bearing Structures, Construction Management and Technology, Traffic Engineering), the Faculty of Civil Engineering offers postgraduate specialist studies (Earthquake Engineering, Project Management in Civil Engineering, Environment Protection in Civil Engineering) and a doctoral study programme (Civil Engineering).

The Faculty of Electrical Engineering was established in 1978. Apart from three-year undergraduate study programmes (Electrical Engineering, Computer Sciences) and two-year graduate study programmes (Communication and Informatics, Power Engineering, Computer Sciences), the Faculty of Electrical Engineering offers several postgraduate specialist study programmes (Process Computing, Advanced Communication Technologies, Power Engineering Networks in Market Environment) and doctoral study programmes (Power Engineering, Communication and Informatics).

The Faculty of Food Technology was established in 1976. Apart from a three-year undergraduate study programme in Food Technology and two-year graduate study programmes (Food Engineering, Food Science and Nutrition, Process Engineering), the Faculty of Food Technology offers several postgraduate specialist study programmes (Safety and Quality of Food, Technology of Traditional Meat Products, Nutrition) and a doctoral study programme (Food Engineering).

The Faculty of Medicine was established in 1998. Apart from a three-year undergraduate programme and two-year graduate study programmes (Nursing, Biomedical-Laboratory Technologies) and a six-year long first degree study programme in Medicine, the Faculty of Medicine offers several postgraduate specialist study programmes (Clinical Epidemiology, Anaesthesiology, Resuscitation and Intensive Care Medicine, Ultrasound in Clinical Medicine – Cardiology, General Internal Medicine, Ophthalmology and Optometry), as well as a doctoral study programme (Biomedicine and Health).

The Department of Biology was established in 2005. Apart from a three-year undergraduate study programme in Biology and two-year graduate study programmes (Biology and Chemistry Education; Biology: Scientific Programme; Nature and Environmental Protection), the Department of Biology offers postgraduate specialist studies (Nature and Environmental Protection), as well as two doctoral studies: Nature and Environmental Protection in collaboration with the Ruđer Bošković Institute and Molecular Biosciences in collaboration with the University of Dubrovnik and the Ruđer Bošković Institute.

The Department of Chemistry was established in 2005. It offers a three-year undergraduate study programme in Chemistry and a two-year graduate study programme in Chemistry Education.

The Department of Physics was established in 2005. The Department of Physics offers a three-year undergraduate study programme in Physics and a two-year graduate study programme in Physics and Informatics (Teacher Training).

The Faculty of Economics was established in 1961. Apart from three-year undergraduate study programmes (Entrepreneurship, Financial Management, Marketing, Management, Business Informatics) and two-year graduate study programmes (Entrepreneurship; Economic Policy and Regional Development; Financial Management; Marketing; Management, Business Informatics, Commerce and Logistics), the Faculty of Economics offers several postgraduate specialist studies (Entrepreneurship, Organisation and Management, Development Management, Finance and Banking, Marketing of Special Areas, Marketing in ICT Environment, Public Services Management), as well as two doctoral study programmes (Management, Entrepreneurship and Innovativeness).

The Faculty of Education was established in 1998. The Faculty offers a five-year long university graduate study programme in Primary Education, as well as a three-year undergraduate and a two-year graduate study programme in Preschool Education.

The Faculty of Humanities and Social Sciences was established in 1961. It offers undergraduate (Bachelor) programmes in Croatian Language and Literature (single degree programme and dual degree programme), German Language and Literature (single degree programme and dual degree programme), English Language and Literature (dual degree programme), Philosophy (dual degree programme), History (dual degree programme), Pedagogy (dual degree programme), Psychology (single degree programme), Information Sciences (single degree programme), Hungarian Language and Literature (dual degree programme), as well as graduate (Master) programmes in Croatian Language and Literature (single degree programme with specializations in Teacher Training or Research in Literature Studies), Croatian Language and Literature (dual degree programme with specializations in Teacher Training or Research Studies), German Language and Literature (single and dual degree programme with specializations in Teacher Training or Translation Studies), English Language and Literature (dual degree programme with specializations in Teacher Training, Translation and Interpreting Studies or Philology), Philosophy (dual degree programme), History (dual degree programme), Pedagogy (dual degree programme), Psychology (single degree programme), Information Sciences (single degree programme), Hungarian Language and Literature (dual degree programme) and Publishing (dual degree programme). The Faculty of Humanities and Social Sciences also offers the following PhD programmes: Linguistics, Literature and Cultural Identity, Pedagogy and Culture of Modern School.

The Faculty of Kinesiology was established in 2020.

The Faculty of Law was established in 1975. Apart from a five-year long first degree study programme (Law) the Faculty of Law offers several postgraduate specialist study programmes (Management of Local and Regional Self-Government Development, Criminal Law, Human Rights) and a doctoral study programme (Law).

The Catholic Faculty of Theology in Đakovo was established in 2005. Apart from a long first degree undergraduate and graduate programme in Philosophical and Theological Studies, the Catholic Faculty of Theology offers postgraduate specialist study programmes (Family Pastoral Care, Crisis Pastoral Care, and Pastoral of Parish Community).

The Faculty of Tourism and Rural Development developed from the Polytechnics of Požega and joined the University of Osijek in 2022.

The Academy of Arts and Culture was established in 2004.

The City and University Library in Osijek (GISKO) was founded on February 8, 1949 as a public library, continuing the tradition of public libraries and reading rooms in the city of Osijek from the mid-19th to the first half of the 20th century. In 1975, it expands its activities with the founding of the University of Osijek and takes over functions and tasks of the central university library, by changing its name into the City and University Library in Osijek. In 1986, its status granted in 1975 was confirmed as a main library for all public and school libraries of the municipality of Osijek and the region of Slavonia and Baranja, and for higher education and special libraries of the University of Osijek and the region of Slavonia and Baranja.

The library has a dual function: it serves as a public/city library and university/scientific library and develops into a general scientific multi-purpose library.

GISKO collects, preserves and provides access to information sources on different media (printed materials: books, magazines, newspapers, etc., AV materials, electronic media, etc.). The information sources are organized into free-access collections (reference library, a collection of scientific and professional literature in the Croatian and foreign languages, a collection of materials belonging to the Austrian Reading Room, a collection of periodicals, a collection of fiction) and special collections: a collection of Deposit copies of the Republic of Croatia, a collection of master’s theses and doctoral dissertations of the Josip Juraj Strossmayer University of Osijek, BDI (Librarianship-Documentation-Information) collection, local collection, memorial collection. It provides loan service and use of materials for its users in the reading room, information and referral services, work on computers and access to online databases and other electronic resources, interlibrary loan services, reprographic services and education services users.

The materials database and services are intended for the broadest range of actual and potential customers – the citizens of Osijek and Osijek-Baranja County and the students, professors, scientific, technical and other employees of the Josip Juraj Strossmayer University of Osijek.

As the central university library, GISKO supports study programs for all three levels of university studies (undergraduate, graduate and postgraduate studies), scientific work at the University, but also the wider community and takes care of the establishment and functioning of the library information activities at the University.

The Student Center in Osijek as constituent unit of the University of Osijek takes care of student standard of life through nutrition, accommodation, occasional and part-time employment, and the cultural and athletic life of students. The subsidized nutrition of students is organized in two large student self-service restaurants in Osijek and a number of smaller canteens with fast and simple services that are located at some faculties in Osijek. The existing capacities (about 6,000 meals daily), which are offered in restaurants of Student Center in Osijek meet the current needs of students.

Student accommodation is organized in adequate conditions in the typical dorm room, rooms for the disabled and apartments for visiting professors. In cooperation with the Student Center in Osijek, there are various sports and other activities organized for students in Đakovo.

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Establishment of the Centre for the improvement and quality assurance of the Josip Juraj Strossmayer (abbreviated: Center for Quality) in January 2014, a result of the development of a systematic approach to quality higher education at the University lasts from 2006. The insurance system and improving the quality of the University is based on the Standards and Guidelines for Quality Assurance in the European Higher Education Area (ESG) and is structured in accordance with the requirements of ISO 9001 for the management of teaching, scientific research and business processes.

Tera Tehnopolis Ltd. is a member of the University of Osijek specialized in development of knowledge-based economy by implementing significantly improved technologies. Tera Tehnopolis was established in 2002 as a joint-venture of the University of Osijek, the City of Osijek and the Osijek-Baranja County to intensify commercialization of publicly funded research conducted at the Josip Juraj Strossmayer University of Osijek; to achieve balanced regional development and retain entrepreneurial and skilled labor force in the region.