Dozens of officers with assault rifles descended on the school and more than 13 police cars went to the school after the alarm was raised about 11am.
Bystanders were asked to move away, the school was placed in lockdown and the pupils were rushed inside the hall.
A person was seen in the school grounds, the gun was not presented at anybody and no threats were made.
The male was seen exiting the school grounds towards Memorial Avenue.
Burnside High School principal Warwick Maguire said the incident was sparked by students who reported "a man walking through school grounds who was acting a little bit unusually.''
He said: "We were approached by some students who felt they should report it to the school. They also thought he was carrying something but they didn't know what it was _ they thought it could have been a weapon, maybe. It was all a bit vague.
"We cleared the grounds of any students and put them into classrooms and phoned police. They advised to keep the children in their classrooms until they had a chance to sweep the grounds.
Paul Beecroft, 44, was sleeping after a night shift when he was woken by police sirens outside his Guildford St home.
"I poked my head out the window and saw the street lined with police cars and officers arming themselves.''
Parents gathered outside the school after receiving messages from their kids saying the school was in lockdown.
Lisa Hartley got a text from her daughter Grace,13, saying her class had been put in lockdown.
"I was scared. I rushed straight down and didn't know what was happening.
Student Leon Davies, 14, said he was changing outside for gym when the principal came over the loud speaker and ordered everyone inside. "About 70 of us got in the gym. It was pretty scary at first.
"We stayed there for about half an hour and we felt safe being all together and then it was all over.
