But now that he actually will be president, Trump says he won't recommend prosecution of Clinton, who he told New York Times reporters has "suffered greatly."
What's more, he said the idea of prosecuting Clinton is "just not something I feel very strongly about."
The quotes come from the tweets of New York Times reporters Mike Grynbaum and Maggie Haberman, who attended a meeting between the President-elect and reporters and editors at the paper.
"I don't want to hurt the Clintons, I really don't," Trump said, according to the tweets. "She went through a lot and suffered greatly in many different ways."
It's a stunning departure from the campaign rhetoric, which could come as a shock to some of the President-elect's most ardent supporters. The Times characterized one exchange as extending an olive branch to Clinton supporters.
"I think I will explain it that we, in many ways, will save our country," he said.
He said the issues have been investigated "ad nauseum" and he added, according to Haberman, that people could argue the Clinton Foundation has done "good work."
The about-face on his formal rival and suggestion that the Trump administration will not pursue further investigations of Clinton related to her private email server or the Clinton Foundation first came Tuesday morning from Trump's former campaign manager Kellyanne Conway, who said it would send a message to other Republicans.
"I think when the President-elect, who's also the head of your party, tells you before he's even inaugurated that he doesn't wish to pursue these charges, it sends a very strong message, tone and content" to fellow Republicans, Conway said in an interview on MSNBC's "Morning Joe."
At the second presidential debate in early October, Trump threatened Clinton, saying that "if I win, I am going to instruct my attorney general to get a special prosecutor to look into your situation."
Conway said Clinton "still has to face the fact that a majority of Americans don't find her to be honest or trustworthy," but added that "if Donald Trump can help her heal, then perhaps that's a good thing to do."
"Look, I think he's thinking of many different things as he prepares to become the president of the United States, and things that sound like the campaign are not among them," she added.
Steve Vladeck, CNN legal contributor and professor at the University of Texas School of Law, said it was unusual for a President-elect to take such a public position on whether to pursue an investigation.
"Even though the attorney general reports to the president, the Department of Justice is meant to exercise a degree of independence from the White House entirely to avoid the perception that political considerations, rather than legal ones, are behind decisions to (or to not) prosecute," Vladeck said in an email. "Indeed, we've seen plenty of scandals throughout American history in which presidents have wrongly politicized the Justice Department's role, and President-Elect Trump's comments don't exactly augur well for preservation of the line between law and politics over the next four years."
Despite Trump breaking a campaign promise to some of the most fervent anti-Clinton supporters, Democrats also took issue with the decision as a sign of the President-elect's executive overreach.
"That's not how this works. In our democracy, the President doesn't decide who gets prosecuted and who doesn't," Sen. Chris Murphy of Connecticut wrote on Twitter
During Trump's ferocious election fight with Clinton, chants of "lock her up" -- referring to Clinton -- became a refrain of the Republican's campaign, as he hammered the Democratic presidential nominee over her decision to use a private email server as secretary of state, and lobbed accusations of corruption and "pay to play" politics at the Clinton Foundation. Trump's choice for national security advisor,
Michael Flynn, also led a high-profile chant at the Republican National Convention of "lock her up."
Trump repeatedly brought up jailing Clinton on his own, often at raucous campaign rallies over the summer and into the fall.
"Remember I said I was a counter-puncher? I am," Trump said at a San Jose, California, rally in June, referencing an anti-Trump speech Clinton gave. "After what she said about me today, her phony speech, that was a phony speech. It was a Donald trump hit job. I will say this: Hillary Clinton has to go to jail, OK? (Cheers) She has to go to jail, phony hit job. She's guilty as hell."
"She gets a subpoena, she deleted the emails, she has to go to jail," Trump said at a Lakeland, Florida, rally in October.
But in interviews with the Wall Street Journal and CBS' "60 Minutes" after the election, Trump refused to say if he would fulfill that commitment to appoint a special prosecutor.
"I'm going to think about it," he told "60 Minutes." "I feel I want to focus on jobs. I want to focus on health care, I want to focus on the border and immigration and doing a really great immigration bill. And I want to focus on -- all of these other things that we've been talking about." He told the program she "did some bad things" but added the Clintons are "good people."
And Trump told the Wall Street Journal
that "it's not something I've given a lot of thought, because I want to solve health care, jobs, border control, tax reform."