The Faculty of Computer Science and Engineering (FCSE) is the result of the unification of the two largest institutions in the area of informatics and computer technologies in Macedonia – the Institute of Informatics (II) at Faculty of Natural Sciences and Mathematics and the Institute of Computer Technics and Informatics at Faculty of Electrical Engineering and Information Technologies (ICTI).

In the given form, the two institutes are working since the eighties of the last century. II started to work in the distant 1985 year as equitable integral hole of the reunited FNSM under the name Institute of informatics. ICTI originates from the Cathedrae of Technical Cybernetics. In was promoted to the level of a Department in 1982 and then grew into an Institute.

As a result of the extraordinary efforts of their members, and in trend with global growth of the informatics field, this period of nearly 30 yearsfollowed with a continuous growth of the scientific and technical capability of these two institutes. The costantly increasing student interest in thisarea and the development of the two institutes, have led them to becoming the most prominent at ther respective faculties and to serve nearly 50% of the students.

Throughout the period of development, there were many joint projects and research activities, on both personal as well as on institutional basis.Both institutes were in a constant race for improving the quality of the studies, scientific research and applications. This race resulted the end, in one final unifying factor - significant development and growth of informatics in Macedonia and the formation of an extremely strong community ofteachers focused on informatics. Since 2011 they formally begun to walk the path together as the strongest and most advanced scientific researchand educational institution in Macedonia in the field of informatics – the Faculty of Computer Science and Engineering (FCSE).