An earlier court proceeding had determined that the man risked persecution or torture if returned to Guatemala but also feared returning to Mexico, where he says he was raped and extorted.
The Trump administration appears to be complying for the first time with a federal judge's order to return a migrant from a foreign country to the United States.
A federal judge denied a request from the Department of Homeland Security to reconsider a court order demanding the return of a immigrant who was deported to Guatemala.
The man fled persecution and torture in Guatemala, he said in a court declaration, and was later raped and targeted for being gay in Mexico while on his way to the U.S. to claim asylum.