Melvin Benn, managing director of Festival Republic, said he needed to prioritise work with other festivals as well as his new role as Chairman of Wembley Stadium.
Festival Republic took up the license and management of Glastonbury in early 2002. In a statement it said the split with Glastonbury founder Michael Eavis had been "mutual and cordial".
Festival Republic's interest in GFL 2011, the company which runs Glastonbury, will be passed to its parent company LNG.
Benn said: "From an operational point of view, myself and my team have taken the festival as far as we can and it is time for a change I think. It has been a wonderful journey with Michael but Latitude, Berlin, Hove and Electric Picnic, none of which existed in 2002, are my priorities, alongside maintaining Leeds and Reading as the bastions of the festival calendar they are, not to mention my demands at Wembley."
"That said I am committed to ensuring as smooth a handover as possible to the new team in Pilton and enjoying Glastonbury for many years to come as a festivalgoer myself."
Michael Eavis said: "I’ll be sorry to see [Benn] go but he has masses of responsibility with all of his shows across the world and now is a good time to part company. I’ve got just about the best team in the business and [my daughter and son-in-law] Emily and Nick are heading up the next generation to take on more responsibility as well."
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