The deportations took place despite a US federal judge granting a temporary suspension of the expulsions order, apparently as planes were already headed to El Salvador.
"Today, the first 238 members of the Venezuelan criminal organization, Tren de Aragua, arrived in our country," Bukele said Sunday morning on X, sharing a video of several men in handcuffs and shackles being transferred from a plane to a heavily guarded convoy.
Trump signed an order invoking the Alien Enemies Act of 1798 on Friday, but it was not publicly announced until Saturday.
The wartime authority allows a president to detain or deport citizens of an enemy nation, and has been invoked only three times before -- during major international conflicts, including World War I and II.
Bukele, in a meeting last month with US Secretary of State Marco Rubio, had offered to house prisoners from the United States in his country, including members of Tren de Aragua and Salvador's own MS-13 gang.
Bukele said the alleged gang members had been sent to the country's maximum security Terrorism Confinement Center (CECOT), a mega-prison on the edge of a jungle 75 kilometers (45 miles) southeast of San Salvador with capacity for 40,000 prisoners.
Inmates at the prison are packed in windowless cells, sleep on metal beds with no mattresses are forbidden from having visitors.
Rubio said in a separate statement Sunday that "hundreds of violent criminals were sent out of our country."
"I want to express my sincere gratitude to President Nayib Bukele of El Salvador for playing a pivotal role in this transfer," Rubio said.
He added that as part of the transfer, the United States had also deported "top leaders" of MS-13, "plus 21 of its most wanted to face justice in their homeland."
Trump, in his order, claimed Tren de Aragua was "conducting irregular warfare against the territory of the United States both directly and at the direction, clandestine or otherwise, of the Maduro regime."
The statement gives Trump's Attorney General Pam Bondi 60 days to enact the ruling making all Tren de Aragua gang members "subject to immediate apprehension, detention and removal."
The detention and expulsion order will apply to all Venezuelan Tren de Aragua members who are over 14 and not naturalized US citizens or lawful permanent residents.
The ACLU and an allied group, Democracy Forward, asked the US District Court in Washington to bar the deportations -- arguing that the 1798 act was not intended for use in peacetime.
Judge James Boasberg on Saturday issued a 14-day halt to any deportation under the new order.
Bondi slammed the ruling, saying in a statement that it "disregards well-established authority regarding President Trump's power, and it puts the public and law enforcement at risk."
The El Salvador prison where the alleged gang members were sent already houses some 15,000 members of the MS-13 and rival Salvadoran Barrio 18 gangs.
They were rounded up under a state of emergency imposed by Bukele after a surge in gang violence in 2022.
Some are serving sentences of over 200 years.