The actress, who has previously appeared in 'Doctor Who', will star alongside Time Lord Smith when the drama returns to BBC One in spring 2010.
The BBC said that Gillan beat off dozens of hopefuls to land one of television's most coveted roles.
It had been speculated that the role might go to Michelle Ryan, best known for her roles in 'EastEnders' and the American remake of 'Bionic Woman', who recently guest starred in the BBC 'Doctor Who' Easter special as a thief called Lady Christina de Souza opposite outgoing Doctor David Tennant.
Gillan previously appeared as a soothsayer in 'Doctor Who' in 2008 in an episode entitled 'The Fires Of Pompeii'. It is not clear if she will return as this character or play someone new.
Gillan said: "I am absolutely over the moon at being chosen to play the Doctor's new companion. The show is such a massive phenomenon that I can't quite believe I am going to be a part of it."
As well as appearing in 'Doctor Who' she has been in episodes of 'Rebus' and 'Harley Street', as well as 'The Kevin Bishop Show'.
Steven Moffat, lead writer and executive producer of Doctor Who, said: "We saw some amazing actresses for this part, but when Karen came through the door the game was up.
"Funny, and clever, and gorgeous, and sexy. Or Scottish, which is the quick way of saying it. A generation of little girls will want to be her. And a generation of little boys will want them to be her too."