The number of homeless students in New York City public schools saw a spike last school year — even as overall enrollment declined, according to new data.

There were 104,000 city schoolkids without stable housing for 2021-22, an increase of 3.3% from the previous school year, shows the state data reviewed by the non-profit Advocates for Children on Wednesday.

More than 29,000 students spent time in shelters last school year, while nearly 5,500 were considered “unsheltered” — staying in cars, parks, abandoned buildings and other unlivable places to call home.

Others stayed with extended family and friends after losing permanent housing or facing economic woes, the report found.

Meanwhile, the nation’s largest school district has been hemorrhaging students, with roughly 120,000 leaving over the last five years.

That’s as the number of homeless kids in the system has likely continued to grow this school year — amid an influx of migrant students without stable homes.

As of last week, more than 6,100 children in temporary housing — many of them asylum-seekers — had enrolled in Big Apple public schools since the summer.

“There’s a lot of attention right now on newly arrived families, as there should be, and there were more than 100,000 students experiencing homelessness before this recent influx,” said Jennifer Pringle, who leads Advocates for Children’s work on student homelessness.

“While the mayor works to address the housing crisis and families seeking asylum, he has to ensure that kids in temporary housing have access to school,” Pringle added.

The highest rate of student homelessness last school year was in the southwest Bronx, where more than 1 in 5 kids were in temporary housing for at least some of the last school year.

Those neighborhoods, which are part of School District 9, are also in one of the areas enrolling the most newly arrived migrant students citywide.

Rates were also notably high last school year in Upper Manhattan and areas of Brooklyn, including Brownsville and Bushwick.

The fastest growing neighborhoods for student homelessness at the time were in Queens — where the number of students in temporary housing skyrocketed by 12.3% over the course of a year. In District 24, including schools in Corona, Elmhurst, Maspeth and Ridgewood, student homelessness ballooned by 21.9% during the school year.

Queens was housing the largest share of asylum seekers in emergency shelters as of earlier this month — 32% of the total migrants, according to Department of Homeless Services data.

“Just a single student in temporary housing is one too many,” said City Councilmember Rita Joseph, who chairs the education committee. “The increase of the student population in temporary housing is extremely concerning — it speaks to the magnitude of the dual housing and migrant crisis our city is experiencing.”

Joseph, who herself has been a foster parent, told The Post she’s going to continue working “to hold the DOE accountable so students in temporary housing get the services that they need and deserve,” alongside pushing for more affordable housing.

Previous data released by Advocates for Children has shown abysmal attendance records and dropout rates for homeless students, especially those living in shelters.

Almost two in three students living in shelters were considered “chronically absent” during the 202-21 school year, the first full school year impacted by the pandemic. That classification means kids missed at least one out of every 10 school days.

They were also more than three times more likely to drop out of high school than their classmates in stable housing.

The report on Wednesday comes as the Department of Education faces persistent vacancies across its dedicated office for students in temporary housing, as first reported by The Post.

The DOE still hasn’t put in place an interim executive director since the office head said he was leaving more than a month ago — a memo earlier this month showed a group of regional directors are leading that team for now.

And the agency has yet to hire 100 shelter-based DOE staffers to work year-round, despite allocating part of its budget for those positions last spring — though central staffer Flavia Puello-Perdomo told The Post last week it would hire the first 50 by the end of this month.

“They say it’s a priority, so let’s see it,” said Pringle.

“If this is a priority, why don’t you have a director responsible for the team supporting students in temporary housing?” she added. “It’s so critical that we get those positions filled — even in the interim.”

Suzan Sumer, a spokesperson for the DOE, said the agency does “vital work” to support students in temporary housing — “none of which will be disrupted while we navigate a period of transition.”

Roughly 350 staffers across the DOE are tasked with supporting students in temporary housing, officials said.

The agency is also “actively seeking candidates” to fill five vacancies out of 18 regional manager positions, which oversee work with homeless students in specific geographic areas.

“It is our on-going priority to provide our students, including students living in Foster Care, Temporary Housing, and Asylum Seekers living in shelters, with the supports and resources they need, when they need them,” said Sumer.