In 1972, he graduated from Perm Military School of the High Command of the Russian Strategic Rocket Forces and later attended KGB intelligence courses in Novosibirsk.

On 7 December 1998, he was appointed Secretary of the Security Council of Russia, and also Chief of the Russian presidential administration.

During this period he was viewed by some analysts as a possible successor to President Boris Yeltsin.

From 1999 to 2003, Bordyuzha served as the Russian ambassador to Denmark.

On 28 April 2003, he was appointed Secretary General of the Collective Security Treaty Organization, a military pact of the Commonwealth of Independent States and held that position until December 2016.