Aberdeenshire Council has had to spend tens of thousands of pounds ridding schools of rodents, birds and insects.
The 2013-14 bill for getting rid of pest infestations was the highest the local authority had faced for three years.
Wasps, ants, slugs, mites, flies and silverfish had to be removed from school buildings.
Specially-trained hawks were also brought in to deal with aggressive gulls.
The council is currently battling a backlog of planned upgrades to crumbling schools.
Between April 2013 and April 2014, pest control expert dealt with 250 cases of infestation, but the local authority insisted children’s education had not suffered.
A spokesman for the council said: “While every effort is made to deter pests, it is inevitable that at certain times of the year there are occasional issues given the rural locations and age of some of our school buildings. However, none of the incidents that have been dealt with over the past few years have caused any disruption to the running of the schools or disrupted in any way the children’s education.”
The local authority’s bill came to £30, 482 in 2011-12, £29,230 in 2012-13 and £38,491 in 2013-14.
Mid-Formartine councillor Paul Johnston said: “Many of our schools are more rural and are likely to have different forms of infestations.
“We’re far more likely to get infestations of wasps or field mice – that’s not in any way a criticism of the council. But, that said, we have a massive backlog in repairs of our estates and it’s something that the Scottish Government has let slide.”
Aberdeen City Council was unable to disclose how much had been spent getting rid of pests, but in one case pupils at Bridge of Don Academy were unable to use the home economics kitchen for a week after a mouse infestation was discovered.
John O’Connell, director of the Taxpayers Alliance, said: “The council is rightly acting quickly to get rid of infestations, but they’ve got to find a more effective long-term solution.
“Calling out the exterminators every time doesn’t seem the most cost-effective way of dealing with the problem.”
In December 2005, Aberdeenshire councillors set out a blueprint to spend £206million on revamping the region’s schools.