Police cordoned off a section of the School Lane off the Brackaville Road as the manhunt was underway.
According to Sean Dillon, Principal of Primate Dixon Primary School, the search included 'a small part' of the school grounds, but that none of the pupils were affected.
"The police were very guarded about what was happening, but thankfully the operation ended shortly after 9.15am and the school day was not affected", he said.
The security operation began after two foreign nationals evaded arrest in Portadown. It is believed one of them was carrying a gun tucked in his waistband.
Police believed that the men and the gun might be in the vicinity of the primary school and conducted a search for them.
A police spokesperson said that the manhunt began at about 3am on Friday morning.
"During the operation, police investigated a Coalisland connection which took them to the vicinity of the school. Police checked a house there and also searched around the school.
"However, neither the men nor the gun were found."