His departure comes during a review of BBC Worldwide's remit led by the BBC's chief operating officer, John Smith, who is due to submit his report by the end of the year.
Depending on Smith's findings, BBC Worldwide, which spans magazine publishing, international TV channels and merchandising and licensing spin-offs such as the Tweenies, could be sold off or have its activities scaled down.
Mark Thompson, the BBC director-general, said: "Rupert has taken Worldwide to record levels of success and the company is now a market- leader in key areas both in the UK and globally. Under his leadership, the company has maximised the value of BBC assets, bringing benefit to licence payers and has successfully grown the BBC name around the world."
BBC Worldwide is the UK's third-largest publisher and has contributed more than £700 million to the BBC's coffers since 1998. According to the BBC's Annual Report published last week, BBC Worldwide returned £141 million to the BBC last year, an increase of 14 per cent on the previous year.
Gavin led the organisation for six years, having joined from BT, and will leave in October. Smith has taken over operational control of BBC Worldwide for the immediate future.