The Faculty of Computer Science of UPH was pioneered by the department of Information Management that began in 1994 under the Faculty of Industrial Technology. This major was later renamed as Information Systems which then became a department under a separate faculty namely the Faculty of Computer Science.

In 1999, the license for Informatics Engineering major was acquired and it was opened with 45 enrolled students in that year. In November 2001, the license for Computer Technology major was acquired, thereby completing the current study programs of the Faculty of Computer Science.

The Faculty of Computer Science was officially established in 2002 with Prof. Dr. Muljono as the first dean .

By the end of 2004, all the three departments within FIK have been accredited by the National Accreditation Board for Higher Education (Badan Akreditasi Nasional – Perguruan Tinggi, BAN-PT).