Thursday's transfer concludes the Obama administration's final push to empty the facility as much as possible prior to Friday's inauguration, with 19 inmates being transferred since Election Day. One of the inmates is going to Saudi Arabia and the other three are being taken in by the United Arab Emirates.
There were 242 detainees at Guantanamo when Obama came into office in January 2009 and he had pledged to close the controversial center within one year in an executive order he signed shortly after his own inauguration. But in recent days, administration officials have acknowledged that this goal was out of reach.
"I don't anticipate that we will succeed in that goal of closing the prison, but it's not for a lack of trying -- that, I assure you," White House Press Secretary Josh Earnest told reporters Tuesday.
Earnest blamed both Republicans and Democrats in Congress for the administration's failure to close the detention facility.
"Because of the obstacles erected by Congress, terrorist organizations have a powerful recruiting tool, and millions in taxpayer dollars are wasted to operate this large facility," he said.
President-elect Donald Trump will now come into office with responsibility for the remaining 41 prisoners.
Four of the remaining inmates have undergone a security review process and are eligible for transfer.
But their transfer, as well as any others, looks unlikely as Trump has slammed the most recent efforts to empty the prison, nicknamed Gitmo.
"There should be no further releases from Gitmo. These are extremely dangerous people and should not be allowed back onto the battlefield," Trump tweeted on January 3, one of several statements about keeping the prison open.
The prison's peak population was 684 detainees in June 2003.
The Office of the Director of National Intelligence, which tracks recidivism among former inmates, said in a September report that nine of 161 inmates released since January 2009 had returned to supporting terrorist groups. An additional 11 are "suspected" of having gone back to terrorist activity, though the report notes that the Defense Intelligence Agency puts that number at 15.