The decision means Khalil must pursue his constitutional claims - including allegations that he was targeted over pro-Palestinian advocacy and unlawfully detained - through the immigration appeals process after a final removal order.
Three judges dissented from the denial of rehearing, writing on Friday that the ruling "imperils the civil liberties of Petitioner Mahmoud Khalil and similarly situated noncitizens" and that "the consequences are profound."
"We cannot fulfill that role if we write ourselves out of relevance and leave the Executive Branch to check itself," the judges wrote.
Khalil's legal team will now go to the Supreme Court.
Last month, Khalil was issued a final order of removal from the Board of Immigration Appeals in a separate case, but his attorneys say other court orders bar the Trump administration from detaining him for the moment.
ABC News contributed to this report.
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