He served as mayor until 2000, when he was elected as governor of Novosibirsk Oblast.

On 6 July 2007 Russia's President Vladimir Putin reappointed him for further five-year term.

In 2010 Tolokonsky resigned as governor and was appointed to the Presidential Envoy to the Siberian Federal District.

He was in office til 2014 when he became a governor of Krasnoyarsk Krai.

Also, as a Presidential Envoy to the Siberian Federal District, he was a member of the Security Council of Russia from 2010 to 2014.