The centre was established on 14 May 2008, it received full accreditation by NATO and attained the status of International Military Organisation on 28 October 2008.

The 2006 Riga summit listed possible cyber attacks among the asymmetric threats to the common security and acknowledged the need for programs to protect information systems over the long term.

Estonia's proposals for a NATO cyber excellence centre received strong support from the alliance's Secretary-General "Jaap" de Hoop Scheffer.

It will help NATO defy and successfully counter the threats in this area.On 30 August 2018, Colonel Jaak Tarien replaced Merle Maigre as the Director of the organisation.

[3] The Cyber Defence Center in Tallinn is one of 21 accredited[4] Centres of Excellence (COEs), for training on technically sophisticated aspects of NATO operations.