An Agreement for Scientific Cooperation was signed with the National Academy of Sciences of Azerbaijan in 1994 and renewed in 2015. In October 2018, a joint workshop was held by the two academies at the initiative of Israel Academy member Prof. Zvi Ben-Avraham and with the participation of leading academics and scholars from both countries. The Azerbaijan delegation was headed by Prof. Fakhraddin Kadirov, head of the Institute of Geology and Geophysics of the National Academy of Sciences of Azerbaijan.

In January 2019, another delegation from Azerbaijan visited the Academy, led by the vice president of the Azerbaijan National Academy of Sciences, Prof. Ibrahim Guliyev. Delegation members met with Academy member Prof. Zvi Ben-Avraham and Dr. Yitzhak Makovsky from the School of Marine Science at the University of Haifa and discussed common areas of interest and potential academic cooperation in the field of gas and oil.