Doğu Karadeniz Kalkınma Ajansı teşkilat yapısı; ''4 Nolu Bakanlıklara Bağlı, İlgili, İlişkili Kurum ve Kuruluşlar ile Diğer Kurum ve Kuruluşların Teşkilatı Hakkında'' Cumhurbaşkanlığı Kararnamesi’nin 190. maddesi uyarınca, Kalkınma Kurulu, Yönetim Kurulu, Genel Sekreterlik ve Yatırım Destek Ofislerinden oluşmaktadır. Aynı kanunun ilgili maddelerine göre Yönetim Kurulu karar organı, Kalkınma Kurulu danışma organı ve Genel Sekreterlik icra organıdır.
Governors, majors, head of general provincial council, chamber of commerce of each city form the Executive Board. The Executive Board is the decision making organ of the Agency. Agency is represented by chairman of the board. The governors of the region alternately shall be the Chairman of the Board according to the alphabetical order of the provinces. The Executive Board consists of 22 members in total.
Concerning regional development objective, Development Council is established in order to enhance the cooperation among public institutions, private sector, nongovernmental organisations, universities and local governments in the region and to direct/guide the Agency. In accordance with the assize of the Council of Ministers dated 15/8/2016 and numbered 2016/9112, the table on the Development Board Member Lists has been abolished.