School has run since February, about the same time the Omicron outbreak breached the South Island.
Holidays begin this week and will be the first extended break since the outbreak began.
Dunedin North Intermediate School principal Heidi Hayward said juggling work had been a "nightmare".
Having pupils off school was not too much of an issue, but staffing was another story.
The pressure on teachers had been "significant" and there was a constant struggle to arrange relief teachers.
There had been some weeks when she had doubts about whether the school could continue to function.
School holidays were coming at the perfect time and would hopefully relieve some of the pressure.
More than 30% of the school had tested positive at some point and it had about 50 pupils home isolating each day.
Nine staff had tested positive and seven had isolated as contacts.
At one stage, five staff had been away for almost two weeks and more than half of staff had isolated for at least one week during the term.
Gore High School had a 29% total infection rate among pupils.
Principal Tara Quinney said the first staff to be knocked out were the cleaners, which left her and her deputy principal cleaning toilets at the end of the day.
Of the 46 staff, 19 had tested positive during the term.
Those left at school were having to pick up slack any way possible.
Rostering year levels off school had allowed staff to manage without too much trouble, but the quality of education for isolating pupils had suffered, she said.
Many pupils had to work off documents uploaded to the internet as there was no capacity to hold classes online as well as in the classroom.
"Teachers can’t be in two places at once."
The holidays would give the school "breathing space".
It was unfortunate some pupils and staff would probably have to isolate during the holidays, but it would help things at the school run smoothly, Mrs Quinney said.
Kavanagh College principal Kate Nicholson said this term had been the hardest since Covid-19 began two years ago.
The school had an absence rate of 20-25% over the past four weeks.
Throughout the term, 29% of pupils had tested positive and 12% of staff.
"We are all hoping for a much more normal term two."
Logan Park High School co-principal Kristan Mouat said last week it had 17 active cases within the school and 60 total cases since the end of February.
It had a roll of 760 pupils.
The school would continue to monitor staffing and would roster year levels home again if necessary.
