The organs of ISESCO are:
The General Conference.
The Executive Council.
The General Directorate.
The general conference shall be composed of the ministers in charge of education, science,culture and communication appointed by their governments, or their represntatives.
The General Conference meets in a regular session once every three years. It may meet in a special session.
The Executive Council is made up of one representative for each Member State, who shall be versed in education, science, culture or communication.
The General Directorate is headed by a Director General, elected by the General Conference for a three-year term, renewable, upon a proposal by the Executive Council. The Director General is the head of the administrative setup of ISESCO and is accountable to the Executive Council and the General Conference. He has direct authority over the entire staff of the General Directorate.
Founding Conference : Fez, 3-5 May 1982 Dr Azeddine Laraki.
The First General Conference : Casablanca, 7-9 June 1983 Dr Azeddine Laraki.
The Second General Conference : Islamabad, 3-5 September 1985 Mr Maya Mohamed Yasin Khan Watu.
The Third General Conference : Amman, 12-15 November 1988 Dr Duqan Al-Hindaoui.
The Fifth General Conference : Damascus, 27-30 November 1994 Mr Muhammad Ghassan Halabi.
The Sixth General Conference : Riyadh, 6-8 December 1997 Dr Khaled Bin Muhammad Lankari.
The Seventh General Conference : Rabat, 22-24 November 2000 Dr Najib Zerouali Ouariti.
The Eighth General Conference : Tehran, 27-29 December 2003 Dr Morteza Haji.
The Ninth General Conference : Rabat, 8-10 December 2006 Dr Habib El Malki.
The Tenth General Conference : Tunis, 2-3 July 2009 Dr Hatem Ben Salem.
The Eleventh General Conference : Riyadh, 1-2 December 2012 Dr Khalid bin Mohammed Al Ankary.
The Twelfth General Conference : Baku, 26-27 November 2015 Dr Abulfas Garayev.
Dr Saleh Bawazir (1st Session, 15-17/11/1982)
Dr Saleh Bawazir (2nd Session, 15-16/1/1983)
Mr Muhammad Ben Abdu Salam (3nd Session, 4-5/06/1983)
Dr Rashed Ben Abdulaziz Al-Mubarak (4th Session, 18-20/09/1984)
Dr Rashed Ben Abdulaziz Al-Mubarak(5th Session, 30/4-4/5/1985)
Dr Rashed Ben Abdulaziz Al-Mubarak (6th Session, 31/8-1/9/1985)
Dr Rashed Ben Abdulaziz Al-Mubarak (7th Session, 1-3/09/1986)
Dr Rashed Ben Abdulaziz Al-Mubarak (8th Session, 7-12/12/1987)
Mr Muhammad Ben Ahmed Al-Uthaimin (9th Session, 7-10/11/1988)
Mr Abdulaziz Ben Sulayman Al Fadhel(10th Session, 27-30/11/1989)
Mr Abdulaziz Ben Sulayman Al Fadhel (11th Session, 3-8/12/1990)
Mr Abdulaziz Ben Sulayman Al Fadhel (12th Session, 19-25/11/1991)
Mr Lamine Kamara (13th Session, 23-27/11/1992)
Mr Lamine Kamara (14th Session, 22-27/11/1993)
Mr Lamine Kamara(15th Session, 19-24/11/1994)
Mr Lamine Kamara (16th Session, 1-5/12/1995)
Mr Lamine Kamara (17th Session, 1-6/12/1996)
Mr Lamine Kamara(18th Session, 29/11-4/12/1997)
Mr Qadi Raqibudin Ahmed (19th Session, 19-23/11/1998)
Mr Qadi Raqibudin Ahmed(20th Session, 22-27/11/1999)
Mr Qadi Raqibudin Ahmed (21th Session, 16-20/11/2000)
Mr Mohamed Abdellah Faris(22th Session, 22-26/12/2001)
Mr Mohamed Abdellah Faris(23th Session, 12-15/12/2002)
Mr Mohamed Abdellah Faris (24th Session, 21-25/12/2003)
Dr Bachir Ahmad Said (25th Session, 24-26/12/2004)
Dr Mabrouk Ghaid (26th Session, 12-14/12/2005)
Dr Mabrouk Ghaid (27th Session, 4-6/12/2006)
Dr Aboubakar Dakoury (28th Session, 9/7/2007)
Dr Aboubakar Dakoury (29th Session, 2-4/7/2008)
Dr Aboubakar Dakoury (30th Session, 27-30/6/2009)
Dr Aboubakar Dakoury (31th Session, 12-14/7/2010)
Dr Aboubakar Dakoury (32th Session, 13-15/6/2011)
Prof. Abdelhadi Boutaleb (Kingdom of Morocco), May 1982 – November 1991.
Dr. Abdulaziz Othman Altwaijri (Kingdom of Saudi Arabia), November 1991 to date.