But the program's future was put in doubt in February when the Department of Homeland Security froze it and announced an internal review as part of President Trump's executive orders aimed at tightening immigration controls.
DHS's termination announcement in the federal register means that the agency will begin the process of notifying families that the minors who had been approved for entry would have to reapply through other immigration channels that could be more difficult.
In addition, 1,465 minors already in the United States under the CAM (Central American Minors) program will not be allowed to renew their status and must go through other means to try to extend their stays.
Immigrant rights advocates condemned a decision that they said would plunge thousands of families into uncertainty.
"Our concern is that the administration is completely abandoning these children and leaving them in a real situation of immediate danger," said Lisa Frydman, a vice president at Kids in Need of Defense.
DHS officials confirmed that the program had been rescinded and cited Trump's executive orders on immigration from January as the impetus.
Carter Langston, a spokesman at U.S. Citizenship and Immigration Services, which oversees the immigration parole system, said the department "will no longer automatically consider parole requests from individuals denied refugee status in El Salvador, Guatemala and Honduras."
The Obama administration launched the program in December 2014 as part of a wide-ranging response to a surge in the number of minors making the often-treacherous journey from the Northern Triangle countries to reach the United States.
That year, more than 60,000 unaccompanied children and about the same number of families entered the country illegally, flooding border patrol stations and adding to already lengthy immigration court backlogs.
Obama aides cited rising poverty, drug trade and gang violence as causes of the spike. The CAM program aimed to provide an alternative path to enter the country for those who were unable to win refugee status or political asylum, either of which often requires applicants to prove they are victims of government-sponsored persecution.
"It was a safety net for children who were in danger but whose parts of their stories might not match a certain class under refugee status," said J. Kevin Appleby, a senior director at the Center for Migration Studies. Appleby said that ending the program "is mean-spirited. It's not a large number of kids, and they're really vulnerable."
USCIS officials said that 99 percent of those who applied won admission to the United States under the CAM refugee and parole programs. They emphasized that the Trump administration's decision to terminate the special parole did not end their chances of coming to the country. Rather, they will now have to apply through the standard parole program that has been in place for far longer.
According to USCIS, those who had won conditional approval under the CAM program but will no longer be permitted entry are 2,444 minors from El Salvador, 231 from Honduras and 39 from Guatemala.
Since Trump took office, the number of people trying to enter the United States illegally across the border with Mexico has plummeted. The president has taken credit for the reduction, and immigrant rights groups acknowledge that Trump's tough immigration rhetoric and DHS's new enforcement policies have had a significant impact.
But they emphasized that the administration is also shutting off important pathways to legal immigration.
"It's the drip, drip, drip of Trump trying to eliminate protection programs," Appleby said.