Sir Cyril was replaced at the helm of the Specialist Schools and Academies Trust (SSAT) in a boardroom reshuffle, although he retains a board place.
Sir Cyril's career stretches back many years and he has been a key adviser to both Labour and Conservative ministers.
He was a driving force behind Tony Blair's academies programme.
As head of the SSAT Sir Cyril has held one of the most influential posts in education, advising four prime ministers and nine education secretaries on policy over the last 20 years.
Sir Cyril could not be reached for a comment, but in a statement made after the surprise announcement of his departure, he said: "The trust has played a crucial and important role over the past 20 years in helping to raise standards in English secondary schools.
"I am delighted to have had the opportunity through the trust to contribute to that achievement."
