The expulsion of the children was carried out under rules that seek to limit the spread of the coronavirus in the United States, show court documents the Justice Department filed Friday.
Since June, however, the administration had refused to disclose the numbers. But in that month it said about 2,000 children had been expelled from the United States.
Meanwhile, immigration advocates had said that many more immigrant children were likely subject to the rules, but it was unclear how many would be expelled until Friday.
On March 21, new border rules came into effect which scrapped decades-old practices under laws meant to protect children against human trafficking and offer them an opportunity to seek asylum in a US immigration court.
The administration argued that the emergency rules aimed to prevent the spread of the coronavirus inside migrant holding facilities and among the broader US population.
US officials have, since March 21, been quickly deporting migrants, including unaccompanied minors, but without standard immigration proceedings.
According to immigration advocates, the new regulations put migrants, especially children, at grave risk.
They have been kept for days or sometimes weeks in hotels with unlicensed contractors with attorneys saying the children's personal information is not recorded in the usual computer systems, making it nearly impossible to track them.
In June, US Customs and Border Protection chief Mark Morgan said border officials had expelled around 2,000 unaccompanied children under the order.
In the same month, the administration was sued by the American Civil Liberties Union which, ever since then, has declined to update the numbers since, citing pending litigation.
The US government said it had expelled 159,000 migrants overall, and 7,600 family units besides 8,800 children forced to leave the country so far.
In April, Trump suspended immigration to the United States, claiming the move is aimed at protecting his people and their jobs during the coronavirus pandemic.
The decision, which has drawn condemnation from Democrats, is in line with one of his long-term policy goals of curbing immigration.
The president promised in 2016 to curb immigration by building a wall on the US border with Mexico, and launched a crackdown on both legal and illegal entries into the country soon after he assumed office.
Democrats and immigrant advocates say Trump’s decision to limit immigration is aimed at distracting people from his response to the current health crisis.