Teachers were concerned for the teenager’s own wellbeing at the Nicolson Institute on Tuesday morning.
The weapon was confiscated.
Onlookers said they saw police activity at the school as officers attempted to apprehend the boy.
Emergency protocol was activated with pupils instructed to remain in their classrooms until the incident was over.
A Police Scotland spokesman said: “Police attended at the Nicolson Institute in Stornoway following concerns raised for a teenage boy.
“Nobody was injured and the matter was dealt with quickly.
“There was no risk to the wider school community.”
“Enquiries are ongoing and Police Scotland is working with the school and Western Isles Council.”
Western Isles Council praised the swift and effective actions of teachers and staff, saying they took correct and appropriate measures with “pupil safety of paramount importance.”
The council said support will be provided for pupils if required.
Donald Macleod, senior education officer with the local authority, praised the swift and effective actions of teachers and staff.
Mr Macleod said “pupil safety is of paramount importance” highlighting school staff took correct and appropriate measures.
He added: “The school immediately applied its policy, making made sure everybody was kept safe throughout the incident and very quickly reported the incident to Police Scotland.”
Police and the school worked together to ensure the matter was dealt with promptly, he added.
School emergency protocol activated in knife alert
21 November 2017
Police were called after a pupil was found with a knife in school.