A federal judge on Friday ordered the Trump administration to release pro-Palestinian activist and Columbia University graduate Mahmoud Khalil from immigration custody.

Khalil, whose plight has been center stage of Trump’s vow to crack down on opponents of Israel’s incursion into Gaza, has been in the custody of immigration agents since March 8.

“After more than three months we can finally breathe a sigh of relief and know that Mahmoud is on his way home to me and Deen, who never should have been separated from his father,” said Khalil’s wife Noor Abdalla.

“We know this ruling does not begin to address the injustices the Trump administration has brought upon our family, and so many others the government is trying to silence for speaking out against Israel’s ongoing genocide against Palestinians,” she said. “But today we are celebrating Mahmoud coming back to New York to be reunited with our little family, and the community that has supported us since the day he was unjustly taken for speaking out for Palestinian freedom.”

Government attorney Dhruman Sampat had argued that Congress has given the executive branch sweeping powers to determine who could be removed from the county.

The courts should not have the authority to interfere, Sampat said.

Mahmoud Khalil, 29, a graduate student at Columbia University, outside the gates of the campus in 2024. Seth Harrison / The Journal News / USA Today Network file

“I don’t think any of that is right,” U.S. District Court Judge Michael Farbiarz said during the remote hearing.

The judge added that there’s “very strong and uncontested record” that Khalil is not a flight risk and poses no danger to the public.

“I’m going to exercise the discretion that I have to order the release of the petitioner in this case,” added Farbiarz, who is based in New Jersey.

Farbiarz declined a government request to put a seven-day stay on his order to give the government more time to possibly fight it.

But it wasn’t immediately clear in the minutes after Farbiarz’s ruling when Khalil could be set free, from his current hold at a detention center in Jena, Louisiana.

Magistrate Judge Michael Hammer said Khalil will have to “surrender his passport and any other travel documents” as a condition of his release.

Judge Farbiarz, though, made it clear Khalil needs to be released from custody on Friday.

Khalil has a green card, is married to a U.S. citizen and has no criminal record.

“No one should fear being jailed for speaking out in this country,” said Khalil’s attorney Alina Das, co-director of the Immigrant Rights Clinic at New York University School of Law. “We are overjoyed that Mr. Khalil will finally be reunited with his family while we continue to fight his case in court.”

Secretary of State Marco Rubio has cited an obscure provision of the Immigration and Nationality Act of 1952 to justify Khalil’s removal, arguing he poses a national security risk.

The Cold War-era statute gives the secretary of state authority to “personally determine” whether Khalil should remain in the country, the administration has argued.

But Khalil’s backers have insisted that the government’s actions are meant to stifle free speech on college campuses and silence opponents of Israel’s ongoing military action in Gaza.

Israeli forces rolled into Gaza shortly after Hamas invaded the country on Oct. 7, 2023, in a terrorist attack that killed about 1,200 people. It’s been estimated that 251 hostages were taken by Hamas terrorists.

More than 55,000 people have been killed in Gaza since Israel launched its war against Hamas.

Representatives of the Department of Justice, Homeland Security and Immigration and Customs Enforcement could not be immediately reached for comment following Farbiarz’s ruling.