It comes as vaccination rules for students continue to evolve, and some teachers and staff are pushing back at the requirement of having the shots in order to work in the schools.
Some teachers held a protest Monday afternoon in Foley Square called "Teachers for Choice." Demonstrators were calling for an end to the city's vaccine mandates for city workers and educators.
Mayor Bill de Blasio called the protocols in place the gold standard -- but that was before the delta variant and before returning to 100% capacity.
Still, schools are moving forward and celebrating.
The confetti flew as anxious children filed into P.S. 25 Bilingual School in the Bronx. Like other NYC public schools, it's now operating at 100% capacity for the first time since March 2020.
When asked which he likes better, being at home or at school, third grader Lucas Goris said, "School because you have more fun than being at home."
Rachel Garcia, 12, already got her first vaccine dose.
"I'm happy to be back at school, because I can study and study more," she said. "So when I get big I can be a lawyer."
But when Eyewitness News asked Isabel Osorio how she was doing, the 7-year-old started crying.
Her father explained he'd rather have her at home.
"I rather them stay at home at least for now, until things start getting back to normal with all the COVID stuff," said Eric Osorio.
And so it went, the kickoff of the 2021-22 school year as New York City begins tries to emerge from the pandemic.
A computer glitch was reported before the opening bell at some schools, and the city's health screening website, where students and staff report their status, was working sporadically.
This appeared to cause delays at the front doors of schools, where people entering had to fill out a screening document manually rather than online.
Asked about the problem during his morning briefing, Mayor Bill de Blasio said he was told the issue had been resolved by around 8:30 a.m. and officials were looking into the cause.
"My understanding is it has been fixed, and it is up and running," the mayor said. "Overload is the obvious answer."
Still, Schools Chancellor Meisha Porter started her back-to-school tour at PS 25 along with mayor and expressed nothing but enthusiasm and optimism.
Porter is defending the district's decision to do away with the remote option, forcing all students back in front of teachers.
She spoke with Eyewitness News earlier Monday morning.
"I've heard a lot from young people about the importance to them of getting vaccinated so they can get to school and experience our new normal of in-person learning," Porter told Eyewitness News anchors Ken Rosato and Michelle Charlesworth. "So I am really encouraged by that."
WATCH: NYC Schools Chancellor Meisha Porter speaks to Eyewitness News on opening day
"We proved it all last year, we proved it during summer again," de Blasio added. "This is the place for kids to be safe, to learn, to be together. It works."
COVID rules are being relaxed this school year as well.
Vaccinated students who test positive but don't have any symptoms won't have to quarantine, and they will be encouraged to keep three feet of distancing.
But some school principals say that's impossible.
Masking is required, and teachers have to get at least one vaccine dose by September 27.
But as of last week, at least 20% still were not vaccinated at all.
Additionally, students in high risk sports and extracurriculars will have to get vaccinated. But the Teacher's union is taking issue with the new school rules.
Unvaccinated school staff and teachers will be reassigned outside of a school building after the deadline, after the city tried to fire them but lost in court.
The UFT says about 80-85% of teachers are vaccinated and is now rushing to get thousands of substitutes ready.
"The mayor's idea of throwing them off a payroll was absurd and disgusting," said UFT President Michael Mulgrew. "I think what we should have learned through the pandemic was to treat people humanely."
Students are also not required to get the shot - and of course, those under 12 can't get it even if they wanted to. That's why some parents are demanding a remote option.
But Chancellor Porter is not budging.
"I understand the concerns that parents have," she said. "That's why we moved to ensure that our entire workforce is vaccinated. So we want to wrap a bubble of protection around all of our students. And again, I definitely understand parents' concerns, but our students - and research has shown - our students have lost a lot over these last 18 months and they need to be back in school."
Under the Vax to School program, students ages 12 and up can get their first dose of the vaccine during the first week of school and get their second dose in October.
The Department of Education says they will be setting up more than 700 vaccination sties at schools around the city every day this week. It's not clear how many adults will actually get the shot.
In the meantime, enrollment is plunging. It is now as low as 900,000, down from over a million before the pandemic.
But the city believes that number will climb.
And regarding teachers, the city must provide accommodations to staff with medical conditions or religious beliefs that preclude them from getting a COVID vaccine.
Many teachers are demanding a remote option and they want the return to full in-person classes delayed until January of next year.
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