That news sent stocks down and political commentators on both sides of the aisle into conniptions. But peeling through the mountains of spin and conflicting explanations about the news can be difficult, so here are the essential facts.
The letter announces that new evidence has been discovered and that the FBI will review those materials to determine whether they are "significant."
Although Comey recommended in July that Clinton not be charged with any crime for her handling of classified materials, the investigation was technically never closed: There are still outstanding issues related to the Freedom of Information Act and disposition of the evidence.
So instead of announcing that he is reopening a case, Comey sent the letter to lawmakers "out of an abundance of caution," a senior law enforcement official told NBC News.
The FBI director had previously testified before Congress that the FBI had completed the investigation component of the case into Clinton's private email server, so Friday's letter was an attempt to update that statement.
Multiple federal officials told NBC News that the emails were discovered in a separate investigation in which the devices of Clinton aide Huma Abedin and her (now estranged) husband, former Congressman Anthony Weiner, were seized.
The FBI has been examining text messages that Weiner sent to a minor in North Carolina. While examining Weiner's laptop, investigators discovered Abedin also used the laptop, which contained some emails between Abedin and Clinton, NBC News reported.
A senior law enforcement official told NBC News that there's no indication that Clinton, her campaign or the State Department were withholding information.
In a Friday evening news conference, Clinton said she was "confident" that the FBI would not recommend charges, and she called on the bureau to provide more information about the emails it is probing.
"You know, we've heard these rumors. We don't know what to believe and I'm sure there will be even more rumors that's why it's incumbent upon the FBI to tell us what they're talking about because, right now, your guess is as good as mine and I don't think that's good enough," Clinton said.
John Podesta, chair of the Clinton campaign, had made a similar argument in an earlier Friday statement.
"We are confident this will not produce any conclusions different from the one the FBI reached in July," Podesta said. In July, the FBI decided to not recommend charges against Clinton for her handling of classified information.
"I have great respect for the fact that the FBI and Department of Justice are now willing to have the courage to right the horrible mistake that they made," Trump said at a rally in New Hampshire. "This was a grave miscarriage of justice that the American people fully understood and is about to be corrected."
Soon after the news broke, Trump campaign manager Kellyanne Conway tweeted that "a great day in our campaign just got even better."
Stocks turned negative after the report of the new probe, as many analysts have said that markets were pricing in a Clinton victory, and that became less likely on the FBI news.
Contracts at PredictIt, which track the chances of a candidate winning the election, saw double digit percentage point swings for both Trump and Clinton. After the news, Trump's chances gained as much as 31 percent, while Clinton's chances fell more than 10 percent. Both contracts have since pared those moves.
After a long campaign season, the Nov. 8 elections were looking to go in Clinton's favor. The former secretary of state led the race by about 4 points, according to a RealClearPolitics average of recent polls that include third-party candidates Gary Johnson and Jill Stein.
Friday's announcement, however, could potentially offer a major political inflection point. Recognizing this, Republican officials immediately went on the offensive.
"This stunning development raises serious questions about what records may not have been turned over and why, and whether they show intent to violate the law. What's indisputable is that Hillary Clinton jeopardized classified information on thousands of occasions in her reckless attempt to hide pay-to-play corruption at her State Department," Republican National Committee Chairman Reince Priebus said in a statement.
"This alone should be disqualifying for anyone seeking the presidency, a job that is supposed to begin each morning with a top secret intelligence briefing," he added.
But even if enough voters disagree with Priebus to hand Clinton the presidency, the pall of an ongoing investigation would likely weigh on the president-elect.
— CNBC's Everett Rosenfeld, Jacob Pramuk, Dan Mangan and AJ Vielma, and NBC News contributed to this report.