Fairbairn and her husband have decided to take time out of their careers to travel around the world with their children.
Fairbairn, a member of the BBC's executive board, was previously on the executive committee led by Greg Dyke. She was formerly a director of strategy for BBC Worldwide.
BBC director-general Mark Thompson said today: "Carolyn has been the driving force behind some of the BBC's most momentous decisions over recent years.
"She was an architect of Greg Dyke's One BBC, led the BBC's prescient move to launch Freeview and was the primary author of our manifesto for Charter Review Building Public Value."
Before joining the BBC in 1997, Fairbairn was a member of the Downing Street Policy Unit with responsibility for policy development in health.
She has also spent seven years working as a management consultant with McKinsey. She has worked as a financial journalist on The Economist and as a development economist for the World Bank.
A BBC spokesperson said today that "it was too soon to say" whether it was seeking a direct replacement.
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