BBC Two controller Jane Root is leaving the corporation to join the Discovery Channel in the United States.
Ms Root recently launched the BBC Two's spring/summer season
Ms Root, who has been in charge of the channel since January 1999, will take up her new post in Washington in May.
She said: "It was a hard decision to make, leaving the BBC and I've completely loved the past five years."
Acting director general Mark Byford said: "We all wish her well with her new job and thank her for her brilliant contribution while here at the BBC."
Ms Root said she was looking forward to her new job.
"Discovery is also a great place, and a special partner to the BBC, so I am really excited about the challenges ahead," she said.
The BBC's partnership with Discovery has produced programmes including Walking With Dinosaurs and its sequel, ratings smash Walking With Beasts and The Blue Planet.
BBC Two has won Channel of the Year twice under Ms Root's tenure, at The Edinburgh Television Festival in 2003 and at the Broadcast Awards in 2004.
"Jane is an exceptional creative talent who has inspired programme makers - both in house and independent - to deliver bigger and better ideas for the audience," said Jana Bennett, the BBC's director of television.
Ms Root is credited with commissioning BBC Two successes including sitcom The Office, architecture show Restoration and Simon Schama's A History Of Britain.
The channel's recent Dunkirk docudrama was also a big winner - it was watched by nearly five million viewers last month, more than double the number who watched BBC One's show Family Business, on at the same time.
Ms Root set up the Independent Commissioning Group (ICG) when she joined the BBC in 1997, which worked with independent production companies.
The group gave the BBC hit shows including The Naked Chef and Dinnerladies.
Root has said in the past that her aim is to make BBC Two "exciting and accessible: a real enjoyable treat".
BBC Two is celebrating its 40th anniversary on 20th April.