The Computer Science Department was established when AAUP opened in 2000 in collaboration with California State University from Stanslos. The department is considered as a distinguish scientific department in the Faculty Engineering and Information Technology as it contributed in enriching the university status locally, regionally and internationally as many students graduated from this department and currently working in different positions.     

The department has qualified professors with rich research and practical experiences and skills to teach students, and this gives students in this department the chance to join graduate programs in Computer Science that will enable them to improve the scientific research in modern ways. This department contributes in developing the information technology in private and governmental sectors in Palestine through graduating qualified students equipped with different required skills. Moreover, the department provides the PhD degree in computer science under collaboration with Palestinian universities.