Currently Managing Director of the independent production company Tigress, Andrew will replace Neil Nightingale, who is standing down after six years in the role to return to programme making.
Jana Bennett, Director, BBC Vision, says: "I am delighted that Andrew is joining the BBC in this important role leading the Natural History Unit, the centre of the best natural history film-making in the world.
"Andrew's own track record demonstrates his enthusiasm and dedication to programmes about the natural world.
"I am confident that Andrew will support the NHU in delivering ever more ambitious projects which deepen our appreciation of natural history and amaze us with the beauty of the world about us."
Andrew will report to Tom Archer, Controller, Factual Production.
Tom Archer says: "I am delighted that Andrew is joining the BBC leading the Natural History Unit. Andrew is a hugely experienced and talented programme maker.
"He is taking over at an exciting time for the department with a number of important projects forthcoming, including Life and Frozen Planet, and I believe he is ideally suited to take the NHU forward to new successes."
Andrew Jackson says: "I'm delighted and hugely honoured to be taking on this prestigious role.
"It has been an incredibly tough decision to leave a company that I've helped build over the last 17 years but opportunities like this come along so rarely.
"It's a huge, exciting job and I'm really looking forward to getting started."
During Andrew's time at Tigress, the company built a worldwide reputation for making outstanding science, wildlife and adventure programmes.
He joined the company 17 years ago to produce and direct the ITV and PBS specials In The Wild, working with, among others, Julia Roberts, Goldie Hawn and Bob Hoskins.
He has been directly involved in producing or directing more than 100 hours of TV and has overseen many more in his role as MD.
He began his TV career in BBC News and Current Affairs before joining the Natural History Unit in 1986.
He worked as a producer-director on several award-winning series for BBC One and Two.
Based in Bristol, the BBC's Natural History Unit delivers a diverse range of natural history programmes on TV, radio, online and for the cinema.
The unit has constantly excelled and created a world-class reputation for ambitious and groundbreaking factual programmes that inform and entertain audiences.
Recent output from the Natural History Unit on TV includes Nature's Great Events, Life In Cold Blood, Planet Earth, the Saving Planet Earth season, Wild China, Big Cat Live, The Secret Life Of Elephants, Lost Land Of The Jaguar, Expedition Borneo, Springwatch, Autumnwatch, Galapagos and Natural World.
On radio, recent series include Nature, Living World, Soundscapes and a major live event, World On The Move.
Andrew will begin his new role in the autumn of 2009.