Until 2003/2004 Qafqaz University was operating in two temporary service buildings. However, a continually increasing number of students, scholars, and researchers (both local and international) necessitated the establishment of a new campus area. Grant programs urging utilization of new facilities and research laboratories, also contributed to this need for an expanded campus, since the previous facilities were not sufficient to accommodate the needs of a growing university with its expanding programs and initiatives.

Therefore, by collaborating with the Azerbaijan authorities and relevant officials, and with the pivotal efforts of the late President Haydar Aliyev, the university was granted The Khirdalan Campus as a new area for operations. The academic year of 2003/2004 was a year in which Qafqaz University celebrated new university buildings in a new location. The total area of the new campus is 28500 square meters.  The new campus, and especially the increased amount of space available in which to pursue academic activities, has been one of the primary factors contributing to the subsequent rapid progress of Qafqaz University in many areas.

As a result, the number of departments doubled, reaching twenty. Student population increased to 2700 - a significant increase. Dormitory buildings and facilities for all types of students needing accommodations while studying at the university were provided in the academic year 2005/2006. A separate building dedicated for language preparation of first year students was built and the Coordinating Unit for Language Teaching came into being.