Pupils were evacuated from the Wensleydale School in Leyburn this morning.
It is understood a threat was left on an answer machine at the school over the weekend.
Children were evacuated when the message was listened to this morning.
Pupils were taken to St Matthew’s Church in the town while police inspected the school.
Police have now left the building.
Inspector Mark Gee was one of several officers who visited the school.
He said: “The school received a suspicious phone call left on an answer machine.
“We visited the school and are now satisfied there is no risk to students or staff.
“We will now be making enquiries to trace those responsible for the call. Obviously making calls of this nature is a serious issue which we will be investigating”
Insp Gee added: “The school has used the incident as an opportunity to follow its polices and procedures which have worked perfectly well.”
In an email to parents, headteacher Julia Polley said: “I took decisive action based on the information I had in my possession.
“Police have been in attendance and declared the site safe. All students and staff have now resumed lessons. There is an ongoing police investigation.
“As soon as I am able to share any further information, I will do so.
“Rest assured your child’s safety is always at the top of my list. I would like to commend the students and staff who acted swiftly and calmly this morning. Also thanks go to St Matthew’s Church, the Leyburn community and Leyburn Primary school for their support.”
Mrs Polley later added in a statement issued by the county council: “We would ask people not to speculate on social media about these issues.”
One student said: “The teachers say they can’t tell us what happened but it’s obvious that it is something bad for us to be evacuated to the church.
“We saw the police going into the school with big black bags.
“The police are going to walk us back to school and we’ve been told we’re going to have an assembly about it.”
Students were led back to school at around 11.45am.
Cllr Patrick Mulligan, North Yorkshire’s executive member for education and skills, said: “ All of our schools have well-rehearsed safeguarding procedures.
“Our health and safety staff supported Wensleydale School this morning and I am very pleased that all steps were taken to ensure the evacuation was carried out safely and according to plan.”