Police and fire crews were called at 1.00pm and the building emptied, but nothing of concern was found.
The emergency services were stood down an hour later.
Officers confirmed they were investigating telephone threats made to a number of schools across the country.
At Glenrothes, pupils mustered at their usual fire drill area before being moved further back as the area was cordoned off.
ACC Steve Johnson said: “A number of secondary schools across Scotland have received a threat via telephone.
“Officers from Police Scotland attended each school and nothing of concern has been found. Our inquiries are at an early stage and will continue.”
He said existing protocols immediately kicked in and he paid tribute to the schools for the way they handled the drama.
“There has been excellent engagement between police and schools over the years in regard to when calls of this nature are received, and the response and assistance provided by each of these schools has been excellent in ensuring an appropriate response and quick reporting.
“Although there is no information to substantiate any of these threats at this time, we are treating this with the utmost seriousness and a thorough investigation is underway.”