The U.S. Central Intelligence Agency's Mission Center for Counterterrorism (often referred to as the Counterterrorism Mission Center or CTMC, formerly the Counterterrorism Center, or simply CTC) is a division of the CIA's Directorate of Operations, established in 1986. It was renamed during an agency restructuring in 2015 and is distinct from the National Counterterrorism Center (NCTC), which is a separate entity. The most recent publicly known Assistant Director for Counterterrorism Mission Center was Chris Wood who led the organization from 2015 to 2017.

The Counterterrorism Mission Center was established as the Counterterrorism Center in February 1986, under the CIA's Directorate of Operations, with Duane Clarridge as its first director. It was an "interdisciplinary" body; many of its personnel and chiefs were drawn from the CIA's Directorate of Operations, but others came from the Directorates of Intelligence and Science and Technology. Observing that terrorism knew no geographical boundaries, the CTC was designed to cut across the traditional region-based bodies of the CIA.

Discredited by the Iran-Contra scandal of 1986, the original aims later gave way to a more analytical role. This did not prevent the Center from contemplating an "Eagle" drone aircraft project in 1986–7, which could have been used to spy on hostage-takers in Lebanon.^{[citation needed]} The idea was unrealistic in terms of the technical abilities of the time. Still, it can be compared to the Predator drone eventually inaugurated in 2000.

Notable early members included Vincent Cannistraro, Chief of Operations and Analysis from 1988 to 1991, Robert Baer, from the Directorate of Operations, and Stanley Bedlington, a "senior analyst."

In the early 1990s, the CTC had no more than a hundred personnel, divided into about a dozen branches. Besides branches specializing in Lebanon's Hezbollah, and secular groups like the Japanese Red Army, another concentrated on Sunni Islamist radicalism, primarily in Algeria. Former CTC Director Cofer Black illustrates the evolution of the organization's priorities throughout the 1990s during the 9/11 commission, explaining:

During the early and mid-1990's, al-Qa'ida was not our principal counterterrorism target. Until September 11, Hizballah had killed more Americans than any terrorist group. The Egyptian Islamic Jihad, Hamas, Shining Path in Peru, Abu Saayef in the Philippines, 17 November in Greece, were all threats to Americans or American interests. Personnel and financial resources, management attention, and policymaker interest were spread among these groups.

In January 1996, the CTC opened the Bin Laden Issue Station to track Osama bin Laden and al-Qaeda, with Michael Scheuer, formerly in charge of the CTC's Islamic Extremist Branch, as its first head. The reasons were similar to those for the establishment of the CTC itself. Unlike the traditional country-based ones, the new station was not geographically limited and drew its personnel from across the U.S. intelligence community.

Geoffrey O'Connell was Director of the CTC from 1997 until Cofer Black became Director in June 1999 as part of a reshuffle by CIA chief George Tenet, who was embarking on a plan to deal with al-Qaeda. At the same time, Tenet made one of his executives, Richard Blee, head of the unnamed section in charge of the Bin Laden Station.