The clip has been shared widely on social media and shows a Levenmouth Academy pupil being assaulted last Friday.
Academy headteacher Ronnie Ross said they were aware of the incident “as soon as it happened” and were working closely with the pupils involved, and their parents.
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He added: “We take all allegations of bullying extremely seriously and, in cases like this, we always involve the Police in our response.
“We dealt with the very regrettable incident in the video immediately and are continuing to work with those involved and their parents.
“These actions can never be condoned, but it’s important for all of us to remember that we can’t understand a full story from a short clip on social media.
“I cannot stress enough that this is not typical behaviour of the vast majority of our young people who work towards our school values of respect, trust, responsibility, teamwork and ambition.”
A Police Scotland spokesperson said: “Police in Fife received a report that a pupil was assaulted, but uninjured, at a school in Leven on Friday, May 17.
“Enquiries have established a number of sensitivities surrounding the circumstances of this incident, and officers continue to liaise with the school and those involved.”