The charges, brought in the federal court in the Eastern District of North Carolina, accuse Comey of threatening the life of the US president and transmitting a threat across state lines.
The case relates to an Instagram post Comey published last May while vacationing in North Carolina showing the arrangement of shells on a beach. In US parlance, the number 86 can be used as a verb meaning to throw somebody out of a bar, while 47 could be seen as code for Trump, the 47th president.
The indictment marks a renewed push by Trump's Justice Department to target perceived political enemies of the president with criminal prosecution.
"I'm still innocent. I'm still not afraid," Comey said in a video posted online after the indictment, adding: "This is not how the Department of Justice is supposed to be."
Comey deleted the May 2025 Instagram message after it attracted controversy.
"I didn't realise some folks associate those numbers with violence. It never occurred to me but I oppose violence of any kind so I took the post down," he said shortly after posting it.
Trump and his allies at the time said they interpreted Comey's post as a threat to violently remove Trump from power.
Acting Attorney General Todd Blanche has moved quickly to carry out Trump's demands for criminal cases after his predecessor, Pam Bondi, was ousted in part for not moving fast enough on them.
Blanche on Tuesday depicted the case as a routine prosecution for a threat against a public official, the type of case federal prosecutors frequently bring.
"While this case is unique and this indictment stands out because of the name of the defendant, his alleged conduct is the same kind of conduct that we will never tolerate, and that we will always investigate and regularly prosecute," Blanche said during a news conference.
US officials investigated Comey in the days following the post and he was interviewed by the US Secret Service, but was not charged.
Trump has for years railed against Comey over his role overseeing an FBI investigation into alleged ties between Trump's first presidential campaign and Russian officials in 2016.
The Justice Department brought a separate case against Comey last September accusing him of lying in congressional testimony about authorising disclosures to the news media about FBI investigations.
A federal judge dismissed the case after finding that the prosecutor who secured the indictment was not lawfully appointed. The Justice Department is appealing the ruling.
The Justice Department for decades sought to preserve distance between the White House and individual criminal investigations. The first case against Comey encountered several legal obstacles.
A federal judge found the lead prosecutor, Lindsey Halligan, may have made serious legal errors before the grand jury that approved the indictment.
Another judge later blocked the Justice Department from using crucial evidence, finding that prosecutors had violated protections against unlawful searches and seizures in the US Constitution. Comey's lawyers said the case was a vindictive prosecution brought to punish Comey for his criticism of Trump, which the defence may revive in the latest case.
"We will contest these charges in the courtroom and look forward to vindicating Mr Comey and the First Amendment," Comey's lawyer Patrick Fitzgerald said in a statement.
