In 1989 the University was relocated to Khartoum due to the devastating civil unrest in Southern Sudan. While in exile the University witnessed enormous expansions on academic and research aspects.
Following the independence of South Sudan on 9th July 2011, the University completely repatriated to Juba. Currently the University hosts 13 schools, 4 Centres, 3 institutes and 2 colleges. These include: School of Art, Music and Drama (SAMD), School of Arts and Humanities (SAH), School of Applied and Industrial Sciences (SAIS),School of Business and Management (SBM), School of Computer Science and Information Technology (SCSIT), School of Community Studies and Rural Development (SCSRD), School of Engineering and Architecture (SEA), School of Education (SED), School of Law (SL),School of Medicine (SM), School of Natural Resources and Environmental Studies (SNRES), School of Public Service (SPS), and School of Social and Economic Studies (SSES); Centre for Distance Education (CDE),Centre for Human Resource Development and Continuing Education (CHRD&CE), Center for Languages and Translation (CLT), and Science, Technology, Engineering and Mathematics (STEM) Centre; National Transformational Leadership Institute (NTLI), Institute of Peace, Development and Security Studies (IPDSS), and French Institute (FI) ; Graduate College (GC) and Kuajok Community College (KCC).