New York City’s public school system has initiated a lawsuit against the Trump administration after the federal government cut millions in funding from local magnet programs. This move is part of a broader campaign targeting policies related to transgender students.

The lawsuit, filed on Wednesday in Manhattan’s federal court, represents a significant escalation in the conflict between the U.S. Department of Education and the nation’s largest school district. For nearly a month, the district had avoided legal action, attempting to negotiate an extension.

Officials in the Trump administration have characterized their actions as a defense of female students’ rights, specifically concerning privacy in restrooms and fairness in sports competitions.

However, the city’s legal team did not hold back in their 48-page lawsuit, criticizing the federal agency for withdrawing support from thousands of students just as the school year began.

The complaint states, “The Department’s sudden reversal, seemingly driven by the Trump Administration’s desire to disrupt the Department’s previously accepted interpretation of Title IX,” referring to the federal law prohibiting sex-based discrimination, “prioritizes politics over public education.”

On September 16, the federal civil rights division informed city schools that it would halt multi-year grants for five magnet programs unless the schools complied with certain conditions. These included separating students in restrooms and locker rooms based on sex and excluding transgender students assigned male at birth from girls’ sports teams.

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 programing 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.

A spokesperson 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.”

Mayor Adams, who controls the city’s school system, has said he would change the exisitng 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 our values,” she said during a recent podcast interview.

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.