US District Judge Carl Nichols in Washington, who was nominated by Trump during his first term, partially granted a request from the largest US government workers' union and an association of foreign service workers who sued to stop the administration's efforts to close the agency.
Nichols's order, which will be in effect until February 14, blocks the Trump administration from implementing plans to place about 2200 USAID workers on paid leave from Saturday and reinstates some 500 employees who had already been furloughed.
It also bars the administration from relocating USAID humanitarian workers stationed outside the US.
Nichols will consider a request for a longer-term pause at a hearing scheduled for Wednesday.
He wrote in the order that the unions had made a "strong showing of irreparable harm" if the court did not intervene.
Nichols rejected other requests from the unions to reopen USAID buildings and restore funding for agency grants and contracts.
The administration in a notice sent to the foreign aid agency's workers on Thursday said it would keep 611 essential workers on board at USAID out of a worldwide workforce that totalled more than 10,000.
"The major reduction in force, as well as the closure of offices, the forced relocation of these individuals were all done in excess of the executive's authority in violation of the separation of powers," Karla Gilbride, a lawyer for the unions, said at a court hearing earlier on Friday.
A Justice Department official, Brett Shumate, told Nichols about 2200 USAID employees would be put on paid leave under the administration's plans, adding that 500 had already been placed on leave.
"The president has decided there is corruption and fraud at USAID," Shumate said.
Trump in a post on Truth Social on Friday accused USAID - without evidence - of corruption and spending money fraudulently.
He said the corruption at USAID "IS AT LEVELS RARELY SEEN BEFORE. CLOSE IT DOWN!"
Hours after he was inaugurated on January 20, Trump ordered all US foreign aid be paused to ensure it was aligned with his "America First" policy.
Chaos has since consumed USAID, which distributes billions of dollars of humanitarian aid around the world.
The State Department issued worldwide stop-work directives after the executive order was issued, effectively freezing all foreign aid with the exception of emergency food assistance.
That brought USAID programs covering lifesaving aid across the globe to a grinding halt, in a move that experts warned risked killing people.
The gutting of the agency has largely been overseen by businessman Elon Musk, the world's richest man and a close Trump ally spearheading the president's effort to shrink the federal bureaucracy.
In the 2023 fiscal year, the US disbursed, partly via USAID, $US72 billion ($A115 billion) of aid worldwide on everything from women's health in conflict zones to access to clean water, HIV/AIDS treatments, energy security and anti-corruption work.
It provided 42 per cent of all humanitarian aid tracked by the United Nations in 2024, yet that represents less than one per cent of its total budget.
