Pupils at a school in Strabane will be taught remotely on Thursday following its closure after a Covid-19 case was confirmed.
Holy Cross College in Strabane said additional cleaning was being carried out in the school.
However, most of the college's 1,600 pupils will return on Friday.
Malone College in Belfast is also due to reopen to pupils then after closing for two days.
Holy Cross principal Clare Bradley took the decision to close the school building to pupils after being informed of a confirmed case early on Wednesday morning.
She told BBC News NI the move was to enable her to contact the Public Health Agency (PHA) and the cleaning service.
That is the protocol for schools in the event of a positive case.
Principals have to contact the PHA to get advice on which other pupils or staff have to self-isolate if they have been in contact with a positive case.
They are also advised to contact the Education Authority (EA) to arrange enhanced cleaning.
In a message to parents, Holy Cross said all pupils would be taught remotely via Google Classroom on Thursday.
Apart from those self-isolating, pupils in years 11 to 14 will return to school on Friday with all pupils returning on Tuesday 29 September following a staff training day on Monday.
Meanwhile, the principal of Malone College in Belfast Katrina Moore told parents the school would reopen as normal on Friday 25 September.
It closed to pupils on Wednesday and Thursday after a teacher tested positive for Covid-19.
In a letter to parents, Ms Moore said closing the school had been a precautionary measure to allow the track and trace process to take place.
A few other schools have also had to close temporarily to pupils since the start of term following staff or pupils testing positive.
However, up-to-date figures on how many schools have had confirmed Covid cases have not yet been released by the Department of Education (DE).
A spokesperson for the DE said: "The department is working with the Education Authority to examine and record existing data sources relating to Covid-19 including information on teacher attendance.
"We are also considering how best to publish this information in an accurate and timely way."