The conservation body, which owns the site near Egham, was granted a possession order to remove a number of squatters from the group Diggers 2012.
Spokesman Simon Moore said they had left the trust's land voluntarily.
He said the group, which sets out to cultivate disused land, grow food and build shelter, were based on land neighbouring the Runnymede Estate.
"It has never been our intention to set up a camp on the National Trust land at Runnymede," Mr Moore said.
"The dispute arose over three tents which were just inside the border of the National Trust land."
He added they were "a community of people who wish to lead a low-impact, sustainable life.
"We are part of a campaign for wider access to disused land in the United Kingdom".
Geri Silverstone, from the National Trust, said: "We certainly respect people's right to protest... we wanted to make sure that they were not getting in the way of other people enjoying that land and restricting access."
The National Trust has been granted a legal order to evict people from the Runnymede Estate in Surrey.