The Supreme Court on Wednesday blocked the Trump administration from ending taxpayer-funded gender treatments for federal inmates, a step Justices Alito and Thomas would have allowed to proceed.
Newsweek reported that the emergency order left the administration’s Bureau of Prisons policy on hold while litigation continues, and the justices offered no written explanation.
Justices Samuel Alito and Clarence Thomas made clear they would have let the policy take effect. The rest of the Court kept the lower-court block in place for now, forcing the federal prison system to keep providing the contested treatments under prior directives.
The fight traces to President Trump’s return to the White House in January 2025. He signed an executive order directing federal agencies to stop using taxpayer money for these interventions, including inside the federal prison system.
The Bureau of Prisons then moved to halt hormone therapy and related surgical procedures previously available to some transgender prisoners. Officials also limited clothing and toiletry items tied to gender identity, shifted focus to therapy and psychiatric medication, and directed staff to use inmates’ legal names or pronouns matching biological sex.
In March 2025, three transgender inmates, one transgender woman and two transgender men held in federal prisons in New Jersey, Florida, and Minnesota, filed suit. They were described as representing around 1,000 transgender people in federal custody and alleged violations of the Eighth Amendment ban on cruel and unusual punishment, equal-opportunity rules, the Administrative Procedure Act, and the Rehabilitation Act.
A federal district court in Washington, D.C., issued a preliminary injunction in June 2025 blocking the policy. An appeals court later denied the government’s bid to lift that order. The Supreme Court took up the emergency matter earlier in the fall.
Alito and Thomas have often stood together on related questions. Readers following their joint dissent in a recent mail-ballot case will recognize the same pattern here: both justices would have let the elected administration’s policy operate while the full case played out.
In an October 9 filing at the high court, the government laid out its core case in plain terms.
"All agree that gender dysphoria is a mental-health disorder, so BOP will address it through mental-health treatment. BOP will no longer address it instead through physical, sex-rejecting interventions (such as sex trait-modification surgeries, hormone interventions in general, and social accommodations), which rest on clinical standards that have been widely discredited and which raise serious security and prison-administration concerns,"
That brief framed the policy as straightforward: treat a mental-health condition with mental-health tools, stop physical interventions the administration says lack sound clinical footing, and protect prison security and orderly management.
White House spokeswoman Allison Schuster did not say much after the ruling.
"This order is a loss for common sense. Since the President’s very first day in office, he has fought to halt the U.S. taxpayer funding of transgender mutilation of prison inmates, and the waste of taxpayer resources on so-called ‘social accommodations,’"
She added that the administration will keep pressing to stop the waste of taxpayer dollars, restore rigorous science as the guide for health policy, and shield Americans from what she called dangerous, life-altering medical practices paid for by the public.
A Department of Justice spokesperson struck a similar note, stressing the procedural reality.
"While we’re disappointed in the Court’s order, this isn’t a final decision on the merits. We look forward to pursuing our appeal in the DC Circuit to reinstate BOP’s policy that affirms biological reality."
The Bureau of Prisons deferred comment to the Justice Department. For now, the agency must continue care under its earlier directives while the case moves forward in the lower courts.
Justice Thomas has written in other recent matters that sex is an immutable biological characteristic and has criticized language that blurs those distinctions. That view sits alongside his longer record with Alito, including their joint dissent in the 2020 Bostock employment case, where Alito called the majority outcome “preposterous.” Coverage of Alito’s comments on the courage required after Dobbs underscores how both justices have absorbed sustained pressure for holding the line on contested social questions.
Li Nowlin-Sohl, senior staff attorney with the ACLU’s LGBTQ & HIV Project, welcomed the order for the plaintiffs and for transgender people in Bureau of Prisons custody.
"This is a critical ruling for our clients and all transgender people in Bureau of Prisons custody,"
She argued that denying what her side calls medically necessary care, including gender-related interventions, violates fundamental constitutional rights and pledged to keep defending the clients and other incarcerated people.
Those competing claims remain unresolved on the merits. The emergency order did not decide whether the Constitution or federal statutes require prisons to supply hormones, surgeries, or identity-aligned social accommodations. It simply left the district court’s injunction in place for the time being.
Personal accounts of Justice Thomas, from his recollection of Alito’s Yale years to moments that reveal his private resolve, remind readers why his votes draw such attention when the Court divides on culture and law.
The administration’s position is that gender dysphoria should be handled as a mental-health condition, that the contested physical interventions rest on disputed standards, and that prisons have legitimate security and administrative reasons to decline them. Taxpayers fund the federal prison system. The White House argues those dollars should not support procedures it views as irreversible and poorly grounded.
Critics of the Court often treat every interim order as a political score. Senator Cory Booker has gone further, calling the Supreme Court “compromised” and pushing 18-year term limits. An unexplained emergency stay does not settle the legal questions; it only keeps the prior injunction alive while the D.C. Circuit and, potentially, a later full Supreme Court appeal take up the substance.
What the public can see right now is straightforward. An elected administration tried to end federal funding for these prison interventions, ground the policy in biological sex and mental-health treatment, and reduce security complications inside Bureau of Prisons facilities. Two justices would have let that policy operate. The Court as a whole said not yet.
Taxpayers still deserve a clear answer on whether federal prisons must keep paying for contested medical transitions while inmates serve their sentences.