Whitehorn has been a non-executive director of the SECC since November 2010.
He will take over as chairman of the Board of Scottish Exhibition Centre Ltd on January 1 2014.
His appointment follows the retirement of Sir Ian Grant, who held the post for 11 years.
Whitehorn, who was born in Edinburgh, joined the Virgin group in 1987 after being talented spotted by Sir Richard Branson.
He is a non-executive director of Stagecoach Group plc and was previously the president of Virgin Galactic, which plans to offer space tourism to the public.