The story of NCTC began on January 28, 2003. During his State of the Union address to the country, President George W. Bush directed that the Terrorist Threat Integration Center (TTIC) be created. All terrorist threat information analysis was to be merged into one center using the resources from many organizations. On May 1 of the same year TTIC was formally stood up and became the central hub for terrorist threat related information.

In August 2004, President George W. Bush established the NCTC (through Executive Order 13354) in order to build upon TTIC's capabilities. On December 6, 2004, the NCTC officially opened its doors.

The Intelligence Reform and Terrorism Prevention Act of 2004 officially legislated NCTC as part of the Office of the Director of National Intelligence (DNI). On June 15, 2005, this legislation went into effect and gave the center even more duties and responsibilities