Marilyn Wheatcroft, in charge of the department for the past five years, has been told to leave her job at the end of July.
Her team of 250 producers - responsible for making programmes for pre-school through to adult learners - were said to be deeply shocked by the announcement.
The move raises questions about the BBC's plans for education broadcasting as it switches its focus to digital interactive learning."Marilyn has a passionfor education, a lifelong commitment to it," a colleague of Ms Wheatcroft's said. "With education meant to be at the heart of the BBC, not to have a post for somebody with so much experience is nothing short of criminal."
BBC Education is now part of a new department called Factual and Learning.
Staff have been given the choice of either producing material for digital output or continuing to produce educational television programmes - which have been guaranteed a further three years.
More than 1,000 BBC staff will lose their jobs over the next three years.