A Moriah College spokeswoman said the school received confirmation from NSW Health shortly before noon and activated its "COVID-19 Positive Diagnosis School Response Plan".
"In accordance with NSW Health advice, the College has closed whilst contact tracing is conducted, and the school is cleaned and sanitised," she said.
The student last attended the primary school on Thursday, May 21.
The Moriah campus will be closed until next Monday, but teaching and learning will continue through its online learning platforms.
Meanwhile, senior school students at Waverley College were picked up by parents or sent home on private school buses earlier on Tuesday.
"Waverley College is cooperating with NSW Health after we were notified this morning of a possible case of coronavirus COVID-19 in our community, a Year 7 student," a spokeswoman said.
"We immediately activated our critical response to get the boys home quickly and safely. We have been in touch with those students and staff members who were in close contact to the student, and we are awaiting further direction from NSW Health."
The school will be closed for deep cleaning before it is re-opened within two days. The school spokeswoman said NSW Health would also re-test the student to confirm his positive diagnosis.
The Waverley College spokeswoman said the school had been preparing for a coronavirus outbreak "for months" and had procedures in place to deliver online schooling in the event of an extended closure.
A different school student who was identified as a potential coronavirus case last week turned out to have returned a false positive test, NSW Health confirmed on Monday.
Premier Gladys Berejiklian warned parents to expect temporary school closures due to coronavirus cases as schools re-opened full-time this week.
St Ignatius College, Riverview was evacuated last week when a student tested positive.