Giles, who is currently executive producer for the BBC's current affairs department, will take up his new post in mid-March.
He will replace former editor Sandy Smith who was appointed as the new executive editor for The One Show in December.
Giles started his career at the BBC in 1991 as an assistant producer for World Service Radio.
He has since worked on the Nine O'clock News, Newsnight, Panorama, Horizon and on current affairs department series such as Hooligans, BBC Two's White Season, and on BBC's factual drama development.
In his current role, Giles has been responsible for some of Panorama's high-profile undercover investigations.
Giles said: "I'm thrilled to be given the opportunity to lead one of the greatest brands in British TV journalism and delighted to able to put something back into a programme which has enabled me to do so many things.
"It's still right at the heart of the BBC One schedule and - with 48 half-hour and eight hour-slots a year - it's a fantastic opportunity to really make a difference."
Oliver Luft writes for Press Gazette