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Two windows were smashed at Eastchurch Primary School’s St Clements site.
It happened at the back of the £4.3 million building in Leysdown Road just before midnight last Wednesday.
It is thought youths had attempted to break-in. They also damaged a padlock.
Executive head Pauline Shipley said CCTV footage has been given to police.
“We are very disappointed by it,” she said.
“If anyone did see anything, we would urge them to contact the police.”
If you can help, phone police on 101, quoting crime reference XY/022208/13.