In February 2005, the Kingdom of Saudi Arabia hosted the first International Counter-Terrorism Conference in Riyadh at which the late Custodian of the Two Holy Mosques, King Abdullah Bin Abdulaziz Al-Saud called upon the international community to establish an international centre to fight terrorism.

On 8 September 2006, the United Nations General Assembly, acting by consensus, adopted the landmark United Nations Global Counter-Terrorism Strategy. In the Plan of Action annexed to the Strategy the Member States resolve to undertake specific measures to counter terrorism, including measures to address the conditions conducive to the spread of terrorism (Pillar I); to prevent and combat terrorism (Pillar II); to build States’ capacity to prevent and combat terrorism and to strengthen the role of the UN system in this regard (Pillar III); and to ensure the respect for human rights for all and the rule of law as the fundamental basis for the fight against terrorism (Pillar IV).

In the second pillar of the United Nations Global Counter-Terrorism Strategy, the General Assembly “acknowledge[d] that the question of creating an international centre to fight terrorism could be considered, as part of the international efforts to enhance the fight against terrorism.”

The UNCCT was established in September 2011, to promote international counter-terrorism cooperation and support Member States in the implementation of the Global Counter-Terrorism Strategy through a voluntary contribution of the Government of Saudi Arabia.

On 18 November 2011, the General Assembly welcomed the establishment of the UNCCT within the Counter-Terrorism Implementation Task Force (CTITF) Office of the Department of Political Affairs (DPA) in the UN Secretariat and encouraged Member States to collaborate with the Centre (A/RES/66/10).

The Centre became operational in April 2012 following the first meeting of its Advisory Board.

In August 2014, the Kingdom of Saudi Arabia donated USD 100 million to the UNCCT. Other donors of the Centre included the United States of America, the United Kingdom and Germany.

On 15 June 2017, the General Assembly established the United Nations Office of Counter-Terrorism (UNOCT). In resolution A/RES/71/291 the General Assembly “welcome[d] the initiative of the Secretary-General to transfer the current Counter-Terrorism Implementation Task Force Office and the United Nations Counter-Terrorism Centre, together with their existing staff, as well as all associated regular and extrabudgetary resources, out of the Department of Political Affairs of the Secretariat, into the Office of Counter-Terrorism.”

The UNCCT benefits from the advice of 22 members of its Advisory Board, chaired by his Excellency Ambassador Abdallah Yahya A. Al-Mouallimi, Permanent Representative of Saudi Arabia to the United Nations. The Office of Counter-Terrorism's Under-Secretary-General Vladimir Voronkov is the Executive Director of the Centre.

In 2018, Counter-Terrorism Implementation Task Force coordination arrangement was replaced by United Nations Global Counter-Terrorism Coordination Compact.

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