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. Husni Awad	Vice President for Academic Affairs	Chairman
Prof. Majdi Zamel	Assistant Vice President for Academic Affairs	Vice-Chair / General Secretary
Dr. Ra’fat Judeh	Vice President for Gaza Strip Affairs	Member
Dr. Salameh Salem	Dean of Student Affairs	Member
Eng. Saada Shalabi	Director of Information & Communication Technology Center	Member
Dr. Khalil Erekat	Dean of Admission, Registration & ;	Member
Prof. Mohammed Shahin	Dean of Graduate Studies	Member
Prof. Jamal Ibrahim	Dean of Scientific Research	Member
Dr. Zaher Haneni	Dean of Faculty of Arts	Member
Dr. Nabil Al-Mughrabi	Dean of Faculty of Educational Sciences	Member
Dr. Abdel Rahman AL-Silwadi	Dean of Faculty of Administrative and Economic Sciences	Member
Dr. Ameed Bader	Dean of Faculty of Social and Family Development	Member
Dr. Eng. Nael Abu Al-Halaweh	Dean of Faculty of Technology and Applied Sciences	Member
Dr. Maen Sheqwarah	Dean of Faculty of Agriculture	Member
Mr. Ammar Jumhur	Dean of Faculty of Media	Member
Dr. Noor Al-Aqra’	Director of Salfeet Branch	Member
Mr. Jasser Khalil	Acting Director of Planning and Quality Department	Member
Dr. Mohammad Abu Elbah	Academic Assistant/Qalqilya	Member
Ms. Randa Ghuneim Totah	Director of Curricula and Textbooks Department	Member
Mr. Mahmoud Hawamdeh	Director of Open Learning Center	Member
Dr. Atif Asouli	Faculty Member	Member
Dr. Hatem Hussein	Faculty Member	Member
Mr. Mohammad Kassab	Regional Student Council	Member