"He has been a fantastic Secretary of Labor," the President said with Acosta at his side. "I just want you to know this is him, not me."
"We're going to miss him," Mr. Trump added.
"I do not think it is right and fair for this administration's Labor Department to have Epstein as the focus, rather than the incredible economy that we have today," Acosta said. "I told him that I thought the right thing was to step aside."
"It would be selfish for me to stay in this position and to continue talking about a case that is 12 years old," Acosta added.
While Acosta had faced questions previously about the plea deal, the pressure on him ratcheted up this week when Epstein was charged by federal prosecutors in New York with sex trafficking involving minors.
"Jeffrey Epstein abused underage girls for years, operating a scheme in which girls he victimized would recruit others for Epstein to exploit and abuse," said U.S. Attorney Geoffrey Berman.
The new charges raised immediate questions as to why Epstein had seemingly been let off with what critics labeled a 'sweetheart' plea deal.
"We did what we did because we wanted to see Epstein go to jail," Acosta told reporters earlier this week, as he defended his decisions eleven years ago. "He needed to go to jail. And that was the focus.”
But Acosta's explanations did little to quell calls on Capitol Hill for him to leave his Labor post.
"Alex Acosta should not have served in the President's Cabinet," said House Majority Leader Steny Hoyer (D-MD).
"I believe it is the right thing for the country that Mr. Acosta announced his resignation," said Rep. Fred Upton (R-MI).
"This is a step toward justice for the girls assaulted by Epstein," said Rep. Katherine Clark (D-MA), who called the decision 'long overdue.'
"It shouldn’t have taken Acosta this long to resign," said Rep. Nita Lowey (D-NY).