It comes nearly three weeks after the city shut down schools over rising positivity rates. The mayor has decided students can return as long as the positivity rates in the schools remain low.
K-5, Pre-K and 3-K students returned for in-person learning. District 75 special needs programs will return on Thursday.
In Staten Island, schools inside the orange zone that closed due to high levels of COVID-19 will reopen Wednesday.
At a news conference Monday outside P.S. 134, the Henrietta Szold School, teachers union President Michael Mulgrew expressed support for the students' return and confidence in the city's COVID safety plans.
"Our youngest, those with the greatest challenges, those are reopening this week," Mulgrew said. "We are making sure everything is being done to keep people safe."
NYC is now scrapping the previous trigger point of 3% city positivity, but every parent must sign a testing consent form for their child.
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Mayor Bill de Blasio warned parents if they signed up for hybrid learning and do not send their kid to school, they will lose the seat to free up space for other students.
He says that too many students are "holding" seats by being signed up for in-person learning and then attending remotely at home.
"We need the kids in school or signed up for in-person learning, and any family that signed up for in-person learning and does not actually intend for their child to be in school, we respect that, we want you then to be placed into the all-remote education approach, so we can free up seats," de Blasio said last week.
Meanwhile, there is still no plan for students in NYC's middle and high schools to return to the classroom. It will likely not happen this year, and that has parents voicing frustration.
A group of parents and students held a rally Sunday at City Hall Park to demand that middle and high schools in the city are also reopened.
WATCH: Parents of middle and high school students speak out
NYC middle and high school parents stage protest
"Middle schoolers are preparing for high school, high schoolers for college and they are missing out on a huge part of these experiences that will shape their entire future," #keepnycschoolsopen's Carly Maready said.
The demonstrators say they're concerned about the long term effects.
"I don't want to be a year behind when I go to high school, it's important for me to fight for my education now," eighth grader Liza Greenberg said.
Gov. Andrew Cuomo wrote an Op-Ed over the weekend arguing that low positivity rates in schools show it is possible to control the spread of COVID-19 if everyone follows public health guidelines. He said that in every part of the state, infection rates in schools are much lower than in their surrounding communities. He attributes that to safety practices in schools like mask-wearing, social distancing and hand-washing.
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