Post-primary pupils and teachers will be required to wear face coverings in school corridors and other communal areas.
Education Minister Peter Weir said the measure would come into effect on 31 August when schools return full-time.
It follows a similar move in Scotland where face coverings will also be required on school buses.
The use of masks on public transport in NI is still “strongly recommended” under the updated guidance.
Mr Weir said the decision followed further advice he received from Stormont’s chief medical and scientific officers.
“The current public health advice is that the use of face coverings provides some benefits,” he said.
“However, it is not a replacement for frequent hand washing, social distancing where possible, covering your mouth and nose when you cough or sneeze and regular cleaning of surfaces.
“It is also important to remember that evidence suggests that the risk of transmission in schools is relatively low compared to some other settings.”
He added that face coverings were not compulsory for “routine use” in schools.
“However, staff and pupils may wish to use them during the routine school day and this is acceptable,” he said.
“Schools should also be aware that some persons (including some children) are exempt from wearing face coverings.”
On Tuesday, the Association of School and College Leaders called for the UK government to change its guidance about the use of face masks in schools in England.
Prime Minister Boris Johnson said: “If we need to change the advice then of course we will.
“All our scientific advice is that schools are safe, it’s absolutely crucial people understand that.”
A decision about face coverings in schools in Wales is expected to be made on Wednesday.