In 1996, Dustin Higgs was accused of murdering three women at a wildlife refuge in Maryland.
The 48-year-old was the third prisoner this week to undergo a lethal injection at the Terre Haute, Indiana, federal prison.
He was pronounced dead on Saturday at 1:23 AM local time (6:3 AM UK time).
Following a 17-year absence, the justice department resumed federal executions last year.
No president has supervised as many federal executions in more than 120 years.
According to the Death Penalty Research Center, not since the dying days of Grover Cleveland's presidency in the late 1800s has the US government executed federal prisoners during a presidential transition.
The presidency of Mr. Cleveland was also the last time, during his second term in 1896, that the number of civilians executed federally was in double digits in one year.
Since 2020, the number of federal death sentences carried out under Mr. Trump has been higher than in the previous 56 years combined, decreasing by about a fifth the number of federal death row inmates.
None of the remaining roughly 50 men are likely to be executed too soon, with Mr. Biden signaling his intention to end federal executions.
On Wednesday, Lisa Montgomery, the last woman on death row, was executed for murdering a woman who was pregnant.
She cut the infant out of the woman's womb, claiming it as her own.
The first woman to be hanged in almost 70 years was Montgomery.
As the coronavirus pandemic raged through prisons nationwide, federal executions began.
Among those who contracted coronavirus last month were Higgs and former drug trafficker Corey Johnson, who was executed on Thursday.
Some members of the execution teams have also tested positive for the virus previously.
In the killings of Tamika Black, 19; Mishann Chinn, 23; and Tanji Jackson, 21, Higgs was convicted of first-degree murder and kidnapping.
He was found guilty in October 2000 in Maryland by a federal jury.
His death sentence was the first to be imposed in the new age of Maryland's federal government, which in 2013 abolished the death penalty.
The lawyers of Higgs argued that executing Higgs was "arbitrary and inequitable" while Willis Haynes, the man who fired the shots that killed the women, was spared a death sentence.
Two decades earlier, the federal judge who presided over Higgs' trial said he "merits little compassion"
"He received a fair trial and was convicted and sentenced to death by a unanimous jury for a despicable crime."
In a statement after the execution, Shawn Nolan, Higgs' attorney, said that his client had spent decades on death row helping other prisoners and "working tirelessly to fight his unjust convictions"
Mr. Nolan said: "Tonight, by killing Dustin Higgs, the black man who never killed anyone, on Martin Luther King's birthday, the government completed its unprecedented slaughter of 13 human beings."
"There was no reason to kill him, particularly during the pandemic and when he, himself, was sick with COVID that he contracted because of these irresponsible, super-spreader executions."
Higgs' petition for clemency on 19 December stated that he was a model inmate and a loving father to a son born shortly after his capture.
He had a difficult childhood and, when he was 10, he lost his mother to cancer, the petition said.
His lawyers wrote: "Mr. Higgs's difficult upbringing was not meaningfully presented to the jury at trial."