JUST detached five faculties from Yarmouk University to form its academic nucleus. These faculties were: Faculty of Medicine, Faculty of Dentistry, Faculty of Pharmacy, Faculty of Nursing and Faculty of Engineering. Consecutively added to these faculties are Faculty of Science and Arts, Faculty of Medical Applied Sciences, Faculty of Veterinary Medicine, Faculty of Computer and Information Technology, and Faculty of Agriculture.

The University currently hosts ten faculties in addition to Faculty of Graduate Studies and Deanship of Research. Since then, JUST has established itself as a distinct educational institution for higher education. Instruction virtually started in September 1986.