Certain years groups came back to the classroom on Monday, with the full school population set to follow the week after.
Primary seven students, Year 12 and Year 14 pupils - as well as all vulnerable children - were allowed to start their school term on 24 August.
It was the first time many children had stepped foot in a school in Northern Ireland since March - when most children were told to stay at home due to the pandemic.
However, some schools have stayed open throughout for the children of key workers.
As the first set of year groups came back, some parents welcomed the return to school.
Stacey Graham said it was "the right thing to do" as her 10-year-old son John went back to Forth River Primary School in north Belfast.
"For parents like myself who work full-time, we have been trying to balance working, having the fun time with the kids and home schooling. We are not teachers so no amount of home schooling can replace the learning that takes place in the classroom," she said.
"My daughter Lily, who is going into P4, was actually crying this morning because John got to go to school first. She loves the social aspect of it, seeing her friends and meeting people," she added.
"I think it is really important, especially for people from working class communities who are already disadvantaged, to get out there and get as much education as they can."
Brendan Gallagher said he felt confident about the schools returning as he brought his 11-year-old daughter Abigail to St Clare's Primary School in west Belfast.
"We had good communication from the school over the last few weeks," he said. "We have known pretty much what has been happening."
However, Trevor, a father of five from Co Down, took to social media to express his concerns about children returning to school.
"As a family, for us coronavirus is a life or death situation," he said. "My wife who is 32, has been taking immunosuppressants to treat a long-term illness.
Trevor said their five young children were set to return to school, and he thought the risk to children was low - in line with what scientific experts have suggested.
However, he said: "The issue is not that of children dying but of whom they will pass the virus too and the long-term consequences."
Official guidance recommends the formation of protective bubbles for primary school children and pupils in years eight to 10 in post-primary schools.
Stormont's Department of Education said interactions between different year groups of older pupils should be limited.
Peter Weir, the education minister, said schools are "not unsafe places" for children or teachers to attend.
He said: "Very, very few, if any, children will come to harm as a result of attending school, but there is evidence of the long-term harm to children's education, life opportunities, mental health and wellbeing from not attending school.
"There is clear unequivocal evidence that children are less likely to catch Covid-19, where they do most of them will have mild to moderate symptoms and in most cases they will make a very full recovery.
Mr Weir added: "There is a very, very low - indeed an incredibly low incidence - of serious disease within children and they are also less likely to transmit the virus."
Boris Johnson, the British prime minister, has also tried to reassure parents ahead of England's planned return to school.
He claimed the risk of contracting coronavirus in schools is "very small", and that pupils face greater harm by continuing to stay at home.
Scottish schools reopened earlier this month, while pupils in England and Wales are set to return in September.
Additional reporting by Press Association
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