The ruling followed a complaint filed in the early morning by the National Immigration Law Centre, a pro-immigrant advocacy group, on behalf of 10 children ages 10-17.
At a rare hearing over a holiday weekend, the judge had been awakened at 2:35 am local time Sunday and alerted to the case.
Washington, DC-based District Judge Sparkle Sooknanan ordered the administration to halt the deportations for 14 days and called for an urgent midday hearing, saying it appeared the children were in the process of being removed from the country.
President Donald Trump's administration struck an agreement with Guatemala that would allow unaccompanied children to be sent back to the country and planned to start deportations this weekend, one current and two former US officials told Reuters.
Trump, a Republican, kicked off a wide-ranging immigration crackdown after returning to the White House in January.
During the emergency hearing on Sunday, Sooknanan pressed the Department of Justice for assurances that Guatemalan children had not been deported already.
"We're here to try to figure out as quickly as we can what is happening," said Sooknanan.
Justice Department lawyer Drew Ensign said no children had been removed but that some had been loaded onto planes.
Ensign said he believed one plane may have taken off but later returned under the judge's order.
The National Immigration Law Centre's lawyer, Efren Olivares, told the judge that some children still appeared to be aboard planes in Harlingen and El Paso, Texas.
White House Deputy Chief of Staff Stephen Miller criticised Sooknanan for blocking the deportations.
"The minors have all self-reported that their parents are back home in Guatemala," Miller wrote on X.
"But a Democrat judge is refusing to let them reunify with their parents."
Migrant children who arrive at the US border without a parent or guardian are classified as unaccompanied and sent to federal government-run shelters until they can be placed with a family member or foster home, a process outlined in federal law.
Among the plaintiffs was a 10-year-old indigenous Guatemalan girl whose mother had died and who had suffered abuse and neglect from other caretakers, the complaint said.
The girl was detained at a US government shelter in south Texas, the complaint said.
Several of the 10 plaintiffs had expressed fear of returning to Guatemala, the complaint said.
The children have been in shelters or foster care in California, Texas, Pennsylvania and New York, it said.
After blocking the deportations of the 10 plaintiffs on an emergency basis, Sooknanan extended her order to cover all Guatemalan children under the care of the US Health and Human Services Department.
