This article examines the impact of the religious factor on Azerbaijan-Iran relations. Azerbaijan and Iran have historically been in the same cultural and religious basin. This situation continued until the Turkmenchay Treaty of 1828. However, after this process, the two countries went through different political processes, and Azerbaijan has been culturally different since the Tsarist Russian period. This difference reached its highest level during the Soviet Union period, and the state and society gained a secular structure. In Iran, which is in the south, religious understanding gradually became dominant and peaked with the 1979 Iranian Islamic Revolution. These processes prevented both states from becoming a unifying element despite the similarity of religion and sect, and on the contrary, continued to exist as an area of ​​conflict. This situation was reflected in both countries' domestic and foreign policies. Azerbaijan’s close relations with Israel, in contrast to Iran’s developing relations with Armenia, are developments that confirm this hypothesis. Thus, it is seen that the similarity of religion and sect has emerged as a security problem in the relations between the two countries.