A Brooklyn preschool that cost taxpayers more than $10 million — even as it sat empty for years — is slated to finally welcome tots this fall, City Hall said.

The nine-classroom schoolhouse at 129 Van Brunt St. in the Columbia Street Waterfront District will open in September — after a Post investigation revealed the city-run site was one of dozens to be built, but never opened, under previous mayoral administrations.

The massive early childhood education center – which had been scheduled to welcome 135 students by mid-2023 – will bring 45 3-K seats and 18 pre-K seats to the neighborhood following urgent pleas from parents, Mayor Zohran Mamdani announced Monday.

“After years of community demand and demonstrated need for additional child care capacity, the Mamdani administration is moving forward with opening the center after the previous administration left the building vacant,” City Hall said in a statement.

The site cost the city at least $5.8 million in general construction costs — and racked up another $5.8 million in rent payments since 2019, even as it sat empty, according to city planning documents.

Frustrated local families urged the city to make good on its promise to open the center, arguing it would provide a vital alternative to parents shelling out boatloads for private care or trekking a mile or more in the transit-sparse neighborhood for the nearest available early childhood seat.

“This is a huge win for the neighborhood,” said Zach Hetrick, a local dad who has championed the 3-K center’s opening by posting quirky social media content to get the attention of the city.

“We’re shocked, I figured it would take a lot more to be heard and listened to,” he told The Post.

The challenges in finding 3-K and pre-K slots were exacerbated for parents forced to drop off children assigned to different locations, local parent Jessica Setton said.

“The bus doesn’t come,” said Setton, who launched a petition in March to open the site. “Unless you’re under a mile [away] from the schools, one child will always be late.”

The facility was one of 28 facilities identified by The Post as long-vacant “3-K For All” sites first planned under the Bill de Blasio administration, but never opened.

The administration of De Blasio’s successor, Eric Adams, argued it wanted to prioritize “stabilizing providers and increasing enrollment rather than simply expanding capacity.”

A source familiar with the matter claimed the city exercised “caution” in determining whether to open the planned site, out of fear it would “destabilize” the area’s existing child care organizations and private providers, which cost tens of thousands of dollars annually.

The city had also blamed “unmet” demand for early childhood seats as the reason to keep the school shuttered, according to emails obtained by The Post.

“We do not see sufficient unmet demand in this area to support the opening of a new site at this time,” reads an email from the Adams-era Department of Education to one parent.

But demand has surged citywide for 3-K spots in recent years, with overall seat capacity jumping 80.9% to 83.8% from 2023-23 to 2023-24, according to an Independent Budget Office analysis.

The preschools closest to 129 Van Brunt St. similarly saw applications far outpace the number of seats, with 79 tots competing for just 12 slots.

Mamdani’s announcement was made as part of a 2,000-seat addition to the city’s universal 3-K programs across the five boroughs – effectively doubling the city’s earlier expansion program.

Families who submitted 3-K applications this year were set to receive offers on Tuesday. But more than 700 seats added after the April 24 application deadline are still available to be filled through the waitlist process, and families can continue adding themselves to the waitlists across all programs.

“On day eight of this administration, we made a promise to New Yorkers: we would fix the 3-K system and build a city where every family can count on affordable, high-quality child care. Today, we’re delivering on that promise,” Mamdani said.

“Over the past few months, we have opened nine previously vacant child care centers, added thousands of 3-K seats where families need them most and started rebuilding trust with working families across this city,” he added, “and we’re just getting started.”

Neighborhood parents also learned last week that an 18-seat preschool classroom at P.S. 29 would be moved to a newly-opened, long-vacant site at 274 Atlantic Ave. — despite City Hall touting the 63-seat site as having exclusively “new” spot to meet skyrocketing demand.

The decision was bizarrely reversed Wednesday night, according to a copy of a letter sent to P.S. 29 parents and obtained by The Post, and both sites will be open to students next fall.

A spokesperson for the DOE argued the move was part of an ongoing evaluation of 3-K demand, but wouldn’t disclose why the last-minute reversal was made.