A federal judge ordered the Trump administration on Friday to release Mahmoud Khalil on bail, a ruling that would end a three-month detention for Mr. Khalil, the only high-profile pro-Palestinian demonstrator in the United States who remains in confinement.

The ruling is a major victory and relief for Mr. Khalil, a Columbia University graduate and legal permanent U.S. resident who played a leading role in demonstrations at the school’s campus last year.

Mr. Khalil, whose wife and infant son are U.S. citizens, has not been charged with a crime.

Instead, the Trump administration justified holding him by invoking a rarely cited law that allows for the deportation of people who oppose the nation’s foreign policy objectives. Marco Rubio, the secretary of state, accused Mr. Khalil of spreading antisemitism.

A week after he was arrested, the administration added other allegations against him, saying he had made paperwork errors when he applied for citizenship last year.

The judge, Michael E. Farbiarz of Federal District Court in Newark, N.J., had already ruled that Mr. Khalil’s detention could not be justified by the foreign-policy law. On Friday, he found that the remaining allegations against Mr. Khalil did not require that he be detained.

Mr. Khalil was the first of many students, including other legal permanent U.S. residents, to be targeted by the Trump administration. His lawyers have argued that he was arrested because of his pro-Palestinian speech. He had remained in detention even as several students in similar straits were released.

The Trump administration has accused Mr. Khalil of siding with the terrorist group Hamas without providing substantive evidence that he expressed support for the group. Mr. Khalil’s lawyers have cited his comments that antisemitism has no place in the protest movement he has helped to lead.

This is a developing story and will be updated.