That decision was handed down Friday by an arbitrator and is a setback for Mayor Bill de Blasio.
As of now, there's no vaccine mandate for students.
The city says the school district is stocked with personal protective equipment supplies to make sure everyone's protected.
There will also be bi-weekly COVID testing in every school.
Schools Chancellor Meisha Porter spoke to Eyewitness News about getting classrooms up and running again.
"The best learning that happens, happens in-person between students and teachers," Porter said. "We have over 500,000 devices that are Wi-Fi and LTE-enabled in our students' hands, but again we're going to follow the science, we're going to follow the advice of our medical partners. What I'd never do is I would never put any child in a place I wouldn't put my own. So, we're family."
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.
Despite all of the health and safety protocols, there's still plenty of debate about mandatory vaccines and in-person learning. In fact, teachers and parents rallied against it on Sunday.
They rallied and marched. Taking their message from City Hall to Washington Square Park.
Right now, Eyewitness News is told 74% have had their shots. Which leaves a quarter of the teachers and workers without the vaccine and without a classroom.
Parents protesting on Sunday say they will not be sending their children and grandchildren back to school.
"Since COVID, I've lost 13 members of my family. I refuse to send my grandchildren into a school where we don't know if it's safe," grandparent Sandra DeJesus said.
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.
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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