The Vice-President for Academic Affairs chairs the Academic Department. The Department includes the Faculty of Technology & Applied Sciences, the Faculty of Agriculture, the Faculty of Social & Family Development, the Faculty of Economics & Administrative Sciences, the Faculty of Educational Sciences, the Faculty of Media, the Faculty of Arts, Deanship of Scientific Research, Deanship of Graduate Studies, Deanship of Admission, Registration & Examinations, Curriculum & Courses Department, Libraries Department, Open Learning Center and Continuing Education & Community Service Center.

The University adopts the open learning system, which enables students to access education regardless of where they reside. Through this system, students can combine between education and work, and adapt their study plan in accordance with their circumstances. Open learning is based on self-learning and on the independency of the learner, in addition to the use of multi-media comprising written, audio, visual and electronic to enable the students to access text materials wherever they are. The University applies the credit hours' system as well as required /selective courses' method.
Recently, QOU adopted the Blended-Learning system that combines e-Learning with the face to face learning system.

The academic year is divided into:

1. First semester consists of 16 weeks
2. Second semester consists of 16 weeks
3. Summer course consists of 12 weeks

The language of instruction is Arabic, while some courses might be taught in English based on a recommendation from the Academic Council and a decision taken by the University Council.

The main task of the Academic Council is to develop the general academic policy and to evaluate and develop academic affairs at the University. The Council applies the University's laws, regulations and instructions for granting the academic degrees. It is responsible for the evaluation of programs and academic specializations, quality assurance of the academic process, following-up the production of courses, issuing the annual University manual and recommending workshops and conferences in addition to other tasks.

The current Academic Council consists of:

Prof. Ma'zouz Alawneh	Vice President for Academic Affairs	Chairman
Dr. Iyad Abu Baker	Vice President Assistant for Academic Affairs	Member
Dr. Ra'fat Jodeh	Head of the Committee for the Administration of Gaza Branches	Member
Prof. Husni Awad	Acting Nablus Branch Manager	Member
Dr. Salameh Salem	Dean of Student Affairs	Member
Dr. Khalil Iriqat	Dean of Admission, Registration and Examinations	Member
Dr. Salah Sabri	Dean of Faculty of Graduate Studies And Scientific Research	Member
Dr. Waleed Awad	Acting Dean of Faculty of Technology and Applied Sciences	Member
Prof. Zaher Hannani	Dean of Faculty of Arts	Member
Dr. Iyad Shtayyeh	Dean of the Faculty of Educational Sciences	Member
Dr. Yousef Abu Fara	Acting Dean of Faculty of Administrative and Economic Sciences	Member
Dr. Rateb Abu Rahma	Acting Dean of Faculty of Social and Family Development	Member
Dr. Khaled Hardan	Dean of Faculty of Agriculture	Member
Dr. Imad Hodali	Dean of Faculty of Media	Member
Miss. Faten Samhan	Director of the Public & Interntional Relations & Media Department	Member
Mr. Fathallah Jayyousi	Acting Director of Planning and Quality Dept.	Member
Ms. Randa Totah	Director of Curricula and Textbooks Department	Member
Prof. Jamal Ibrahim	Director of Digital Learning Center	Member
Mr. Ma'mon Abu Alia	Acting Director of Continuing Education and Community Service Center	Member
E Eng. Imad Assaf	Director of Information and Communications Technology Center	Member
Mr. Zakaria Saqallah	Academic Assistant / Gaza	Member
Dr. Atef Al-Esoli	Faculty Member	Member
Dr. Hatem Husain	Faculty Member	Member
Mr. Mohammad Kassab	National Student Council	Member