Willis departs as the BBC prepares to begin its Creative Future strategy, which it unveiled in April. The strategy is the BBC's "editorial blueprint" for the next six years and explains how the corporation will respond to a world in which "on-demand" entertainment rules.
BBC director-general Mark Thompson warned at its launch that the BBC risked losing a generation of younger audiences if it did not respond to changing habits. It encompasses plans for a new brand aimed at teenagers and increased focus on new media.
Factual and learning has been hard hit by Thompson's planned 3,700 job cuts with as many as 400 reported lost from the department.
According to Thompson, said: "We talked about various roles for John as we begin to implement Creative Future but he has decided to take the opportunity to retire from the BBC and pursue other avenues. We all wish him the very best."
He added: "John is one of the most respected creative leaders in British broadcasting."
During his time as head of factual and learning Willis was involved in some of the BBC's most notable programmes in recent years including 'Dunkirk', 'Planet Earth', 'The Secret Policeman' and 'Auschwitz'.
Willis said: "Now that the organisation is also planning a BBC-wide restructure, I believe this is the right time for me to retire from the BBC, although certainly not from broadcasting. The full benefits of the new factual and learning structure are becoming clearer and the division is in good shape for the future."
Willis said he fully intends to continue his career in broadcasting. He recently became an external ombudsman for the Guardian.
He began his career as a documentary maker at Yorkshire Television, winning awards for ground-breaking programmes like 'Johnny Go Home' and 'Rampton – the Secret Hospital'.
He is a former Channel 4 controller of factual programmes and created successful new strands like 'Cutting Edge', 'True Stories' and 'Secret History'.
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