The former Columbia University graduate student was freed in Louisiana on Friday after a court ruling.
He is expected to head to New York to reunite with his US citizen wife and infant son, born while Khalil was detained.
"Justice prevailed, but it's very long overdue," he said outside the facility in a remote part of Louisiana. "This shouldn't have taken three months."
The Trump administration is seeking to deport Khalil over his role in pro-Palestinian protests. He was detained on March 8 at his apartment building in Manhattan.
District Judge Michael Farbiarz found it would be "highly, highly unusual" for the government to continue detaining a legal US resident who was unlikely to flee and hadn't been accused of any violence.
During an hourlong hearing conducted by phone, the New Jersey-based judge said the government had "clearly not met" the standards for detention.
The government filed notice that it's appealing Khalil's release.
Khalil was the first person arrested under Trump's crackdown on students who joined campus protests against Israel's war in Gaza.
The Trump administration has argued that noncitizens who participate in such demonstrations should be deported as it considers their views antisemitic.
Protesters and civil rights groups say the administration is conflating antisemitism with criticism of Israel in order to silence dissent.
Farbiarz gave the administration leeway to continue pursuing a potential deportation based on allegations that he lied on his green card application, an accusation Khalil disputes.
The international affairs graduate student served as a negotiator and spokesperson for student activists and wasn't among the demonstrators arrested, but his prominence in news coverage and willingness to speak publicly made him a target of critics.
The judge agreed Friday with Khalil's lawyers that the protester was being prevented from exercising his free speech and due process rights despite no obvious reason for his continued detention.
Khalil said Friday that no one should be detained for protesting Israel's war in Gaza. He said his time in the detention facility had shown him "a different reality about this country that supposedly champions human rights and liberty and justice."
"Whether you are a US citizen, an immigrant or just a person on this land doesn't mean that you are less of a human," he said, adding that "justice will prevail, no matter what this administration may try to portray" about immigrants.
In a statement after the judge's ruling, Khalil's wife, Dr. Noor Abdalla, said she can finally "breathe a sigh of relief" after her husband's three months in detention.
The judge's decision comes after several other scholars targeted for their activism have been released from custody, including another former Palestinian student at Columbia, Mohsen Mahdawi; a Tufts University student, Rumeysa Ozturk; and a Georgetown University scholar, Badar Khan Suri.
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