NEW YORK — New York City’s public schools are suing the Trump administration after it slashed tens of millions of federal dollars from local magnet programs, as part of a campaign against policies for transgender students, officials announced Thursday.

The lawsuit, filed the day before in Manhattan Federal Court, marked a major escalation in the ongoing dispute between the U.S. Education Department and the nation’s largest school district, which for about a month had refrained from legal action while it tried to negotiate for more time to hold onto the grants.

“By trying to unlawfully coerce New York City public schools into changing its policies and violating local laws, the federal government is showing that it does not have the best interest of students and New Yorkers at heart,” Muriel Goode-Trufant, the city’s corporation counsel, said in a statement.

The administration has framed its efforts as a fight for the rights of female students, including their privacy in bathrooms and competitiveness on sports teams — a wedge issue LGBTQ advocates say is a red herring that comes at the expense of transgender youth’s inclusion and mental health.

A spokesman for the U.S. Education Department called the case meritless because the magnet school grant program requires certification of civil rights compliance, “which we could obviously not do in the face of NYC’s continued determination to violate the rights of female students.”

But lawyers for the city minced no words in the 48-page complaint that accused the federal agency of pulling the rug out from under the feet of thousands of students, with the school year already underway.

“The abrupt about-face by the Department, seemingly based on the Trump Administration’s fixation with upending the Department’s previously accepted interpretation of Title IX,” read the complaint, referring to the federal education law against sex-based discrimination, “puts politics before public schools.”

On Sept. 16, the federal agency’s civil rights division notified city schools it would discontinue multiyear grants at five magnet organizations unless it agreed to a number of demands, including to separate students in bathrooms and locker rooms on the basis of sex and ban transgender students who were male at birth from girls sports.

In the days that followed, local education officials let a deadline lapse to make the policy changes.

The stoppage affected 19 magnet schools with 7,700 students, according to the complaint. Lawyers for the city accused the federal agency of skipping procedures required by law before discontinuing the grants, and asked a federal judge to reinstate them.

The move had the “immediate effect” of disrupting schools’ ability to offer specialized programming this school year, due to the loss of $11 million in carryover funds, the suit said. Another $36 million had been promised to the city’s schools for the remainder of the five-year grants, which has now been put into jeopardy.

“The abrupt cancellation of the (magnet school) grants imperils every student’s 2025-2026 school year and unfairly undermines the availability of the unique educational opportunities they were promised when they enrolled,” the complaint said.

Mayor Eric Adams, who controls the city’s school system, has said he would change the existing city policy if he could, but insisted state education law prohibits him from doing so. His schools chancellor, Melissa Aviles-Ramos, has struck a different tone — committing to uphold the gender guidelines as part of the school system’s “values.”

“New York City Public Schools is fighting back against the U.S. Department of Education’s attack on our magnet program and transgender and gender expansive students,” Aviles-Ramos said in a statement.

“U.S. DOE’s threat to cut off tens of millions of dollars in magnet funding unless we cancelled our protections for transgender and gender expansive students is contrary to federal, state and local law,” she continued, “and, just as importantly, our values as New York City public schools.”

Adams’ rhetoric sparked swift backlash in New York, with LGBTQ advocates organizing a protest in lower Manhattan and elected parent leaders pushing the school system to stand firm against any changes to its gender policies.

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