The terrifying attack happened at Walton High on Walnut Tree on Monday, and it has left some parents scared to send their children to school.
A bare-chested male and a female, both estimated to be aged 17 or 18, barged through the open school gate at 3pm, just as lessons were winding down for the day.
"The man had no shirt on. He was carrying a knife and a shovel and he look crazed, like he was on drugs or something," said one eye witness.
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Pupils injured as "crazed" couple barge into school in Milton Keynes
"They ran about bashing things with the shovel, shouting 'M4 is coming to get you'. We think M4 is one of the gangs in Milton Keynes, possibly from Westcroft," she added.
The duo entered the school building and ran through the isolation room shouting threats.
"They started punching three students, all boys, who were in the isolation room. All three boys were injured," said another eye witness.
The pair then ran out of the building and adults managed to restrain the male.
"They got him on the floor, but then he got away and ran back out of the gate. We saw him and the girl get into a waiting car, which drove away," said a student.
A spokesman for Walton High said: "As students were leaving at the end of the school day on Monday, two intruders entered the premises with a view to causing trouble. Staff responded very quickly and commendably dealt with the situation which meant students were protected and the intruders were on the premises for under two minutes. The police were called and are confident arrests will be made. "
The spokesman added: "There is no truth in the rumour circulating that there was a knife involved."
Some parents have questioned the school about future security measures, but are still not happy.
The MK Citizen has contacted Thames Valley Police about the incident but is yet to receive a response.
"It was a terrifying experience for the students and we want to know how these people managed to get into the school so easily and what they plan to do to avoid it happening again... We need to know our children are safe," said one mum.