The pupil has been in self-isolation in recent days and was not infectious when they last attended school, said the health service.
It says the risk to any other students or staff is very low and the school should remain open.
School principal Irene Ogden last night told parents she understood if they wished to keep their children home given the circumstances of the test result.
It's the second school pupil to be confirmed positive this week.
Earlier a senior student at St Dominic's Catholic College was confirmed infected with Covid.
The entire school community has been asked to take a covid test after the girl attended classes for three days last week while infectious.
Surrounding schools asked parents to keep children home who had siblings at the girls' college as a safety measure.
Nearby Liston College, which shares a number of senior level classes with St Dominic's, has revealed a small number of boys have sisters who have been identified as close contacts of the infected pupil.
Principal Chris Rooney said the boys were self-isolating for 14 days. They would be taught through distance learning.
He said the Catholic boys' school has no positive cases of covid.
Both school Covid cases are connected to a bereavement sub-cluster of the Mt Roskill Evangelical Fellowship mini-cluster.
There are now 24 cases from that event with 45 cases linked to the church.
