The Vice-President for Academic Affairs heads the Academic Department. It 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 & Graduate Studies, Deanship of Admission, Registration & Examinations, Curriculum & Courses Department, Libraries Department, Measurement & Evaluation Center, Open Learning Center (OLC), 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: 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:
- First semester consists of 16 weeks
- Second semester consists of 16 weeks
- 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, following-up issuing the annual University manual and recommending workshops and conferences in addition to other tasks.
The current Academic Council consists of:
| Prof. Samir Al-Najdi | Vice President for Academic Affairs | Chairman |
| Prof. Mohammad Al-Titi | Vice President Assistant for Academic Affairs | Vice-Chair / General Secretary |
| Dr. Eng. Islam Amr | Assistant to the President of the University for Technology and Production Affairs/Director of Information & Communication Technology Center / General Supervisor of the Open Learning Center | Member |
| Prof. Mohammed Shahin | The President Assistant for Student Affairs | Member |
| Prof. Jamal Ibrahim | Dean of Admission, Registration & Examinations | Member |
| Prof. Husni Awad | Dean of Graduate Studies & Scientific Research | Member |
| Prof. Abdul-Raouf Khrewish | Acting Dean of Faculty of Arts | Member |
| Prof. Majdi Zamel | Dean of Faculty of Educational Sciences | Member |
| Prof. Thiab Jarrar | Acting Dean of Faculty of Administrative and Economic Sciences | Member |
| Dr. Iyad F. Abu Baker | Acting Dean of Faculty of Social and Family Development | Member |
| Dr. Eng. Waleed Awad | Acting Dean of Faculty of Technology and Applied Sciences | Member |
| Dr. Maen Sheqwarah | Dean of Faculty of Agriculture | Member |
| Dr. Shadi Abu Ayyash | Dean of Faculty of Media | Member |
| Dr. Atieh Musleh | Director of the Planning and Quality Department | Member |
| Mrs. Randa Ghuneim Totah | Director of Curricula and Textbooks Department | Member |
| Dr. Marwan Al-Kawni | Faculty Member - Nablus | Member |
| Mr. Ziad Al-Wawy | Head of Students Council | Member |