A federal judge on Monday halted President Trump’s move to oust transgender service members from the military, saying those troops qualify as a protected class and rejecting Mr. Trump’s claim that his national security decisions shouldn’t be questioned.

The ruling by Judge Colleen Kollar-Kotelly breaks new legal ground for courts in Washington, D.C., finding that transgender status is a “quasi-suspect” legal category deserving of heightened protections by federal courts. She said Mr. Trump’s policy creates an “inherent inequality” that likely violates the Constitution.

And she said the president’s own conclusions about the value and costs of transgender troops were wrong.

“All of the reasons proffered by the president for excluding transgender individuals from the military in this case were not merely unsupported, but were actually contradicted by the studies, conclusions and judgment of the military itself,” she wrote.

Judge Kollar-Kotelly issued an injunction preventing any transgender troops from being discharged or refused the ability to join up — though she did allow the administration’s ban on the Pentagon paying for gender-reassignment treatments to remain in place.

The effect of her order was to revert to the policy that existed before Mr. Trump’s July tweet and later August memo on transgender troops.

Mr. Trump had been trying to reverse an Obama-era change that allowed transgender troops to serve.

On July 26, he abruptly announced via Twitter that he had decided to reimpose a prohibition, then issued a more formal memo laying out his policy decision on Aug. 25.

The memo called for halting “accession” of new transgender troops, and gave the Pentagon until early 2018 to come up with a policy for how to discharge transgender troops already serving.

But Judge Kollar-Kotelly, appointed to the federal district court in Washington by President Clinton, said the new policy illegally singles out transgender troops for different treatment.

She ruled that transgender status is a “quasi-suspect class” when it comes to discrimination law, meaning any policy that targets them faces heightened scrutiny by the courts on the basis of fairness.

That means the government must show a compelling purpose for the disparate treatment — a bar the judge said Mr. Trump fell well short of.

The judge also said even outside of transgender issues, the policy broaches critical gender lines, which would subject it to heightened scrutiny anyway.

“It is well-established that gender-based discrimination includes discrimination based on non-conformity with gender stereotypes,” she wrote.

“The [exclusion] of transgender individuals inherently discriminates against current and aspiring service members on the basis of their failure to conform to gender stereotypes. The defining characteristic of a transgender individual is that their inward identity, behavior, and possibly their physical characteristics, do not conform to stereotypes of how an individual of their assigned sex should feel, act and look,” the judge concluded.

Tony Perkins, president of the conservative Family Research Council and a Marine veteran, said the judge was wrong to reject the president’s national security determinations.

He compared it to the judges who have second-guessed Mr. Trump’s decision-making on his travel ban, where he identified a number of countries the administration said were so deficient on sharing information about their citizens that it was dangerous to admit them into the United States.

“The courts have moved beyond legislating on the invented rights of abortion and same-sex marriage to clearly usurping the constitutional authority of the executive branch,” Mr. Perkins said.

But transgender advocacy groups said the judge’s ruling reassured them.

“More than a year ago, the Department of Defense assured transgender service members it was safe to come out, and it’s unconscionable that President Trump is now targeting them for discrimination. Any qualified American who is willing to serve should be allowed to do so,” said Ashley Broadway-Mack, president of the American Military Partner Association.

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