Children at the Steiner School in Garlinge Green had cultivated the wild fruit trees as part of a Woodland Trust scheme to plant six million trees across the country.
Teacher Larry Klatzko spoke of his anger after the trees were ripped from the ground by their roots.
"Our children were engaged in this activity as a positive environmental deed, and they're quite distraught by what has happened," he said.
He told the Canterbury Times that the school was taking part in the scheme not only as a positive environmental measure, but also to help rejuvenate the area surrounding the school, planting some 840 trees.
"It's something that was meant to enhance their lives. We hoped they could return to the school in years to come and show their own children what they had created," he said.
The trees had cost around £3,000, had been planted along a lane spanning 400 metres of the school's grounds, which is on the site of a former hospital.
The school bought the site in 2011, and as part of the planning application to open a school there, agreed to improve the land.
"We've tried to rejuvenate the area. We wanted to enhance the environment, develop it for permaculture and enable children to learn about the land," Mr Klatzko said.
"We've reported both thefts to the police. The officer I spoke to said, 'so, a forest has been stolen?' It's very strange."
The first batch of 300 trees are thought to have been taken over a 10-day period at the end of March, with a further 400 up-rooted and stolen overnight last Monday (April 22).