A series of incidents occurred as senior pupils marked their final day at the school. Cars were reported to have been damaged, and fights took place in the bus park, with flour, bottles and eggs being thrown.
A Police Scotland spokeswoman said: “Police in Levenmouth have arrested and charged three youths following a disturbance on Friday, April 27.
“Officers were called around 2pm.
“The youths aged 13, 15 and 17 will be referred to the Children’s Reporter.”
Headteacher Ronnie Ross said the incidents spoiled the senior pupils’ final day at the school.
He said: “Friday was the final day for seniors leaving Levenmouth Academy and like most high schools across Scotland our 5th and 6th Year leavers took part in the annual “Muck Up” as it is known.
“Unfortunately other pupils from the school chose to leave the school premises at lunchtime and their behaviour was unacceptable.
“Most of the students were just having fun but I am very disappointed with the behaviour of a few individuals.
“They ruined what should have been a celebration for those who have worked hard throughout their time at Levenmouth Academy and have been a credit to the school.
“The school management were in school at the time and dealing with situations as they arose to the best of their ability.”