The history of relations between Azerbaijan and CERN dates back to the former Soviet Union. During that period, scientists from Azerbaijan took part in CERN experiments, essentially through JINR. After independence Azerbaijan established direct connections with CERN. The first International Cooperation Agreement (ICA) with CERN was signed in 1997.

Following the initiative of the Azeri Ambassador to the UN, who visited CERN in June 2006, and a subsequent visit of the CERN delegation to the Baku Institute of Physics, a new Protocol to the ICA for the participation of Azeri institutes in high-energy physics experiments at CERN was signed in 2007, defining the training of young Azeri scientists (also with the support of JINR) and the support to informatics development as highest priorities. Within this programme, in 2008 the Baku Institute of Physics bought and installed a cluster of 300 decommissioned CERN computers. Scientists from Institutes in Azerbaijan are participating or have participated in the following experiments: ATLAS, NA61/SHINE, NA49 and ALICE.