Turkey's Prime Minister Recep Tayyip Erdogan and Iran's President Hassan Rouhani signed the protocol during their meeting.
The high-level council is planned to happen during Rouhani's visit to Turkey.
Erdogan's visit to Iran's Foreign Policy Institute was cancelled due to a possible of delay in meeting Iran's Supreme Leader Ayatollah Ali Khamenei.
Erdogan met Khamenei for roughly an hour at his residence. He was accompanied by Foreign Minister Ahmet Davutoglu; Economy Minister Nihat Zeybekci; Energy Minister Taner Yildiz; Development Minister Cevdet Yilmaz and Culture Minister Omer Celik.