The Faculty of Computer and Information Science was founded on 1 January 1996 when the previous Faculty of Electrical Engineering and Computer Science was split into two new faculties. However, the undergraduate programme in computer science at the University of Ljubljana started in the academic year 1973/74, first as an elective programme after the second year of electrical engineering study, and since 1982 as an independent four year programme.

In 2014, the Faculty relocated to a new building in Brdo pri Ljubljani. This was the result of a several year-long project to build new facilities for the Faculty of Computer and Information Science and the Faculty of Chemistry and Chemical Technology. It is also the largest project in Slovenia to be co-funded by the European Union and the largest investment in the history of the University of Ljubljana.