James Comey says he is innocent and the charges are politically motivated, as they follow Trump pressure on prosecutors to act.
Former FBI Director James Comey has maintained he is innocent after being charged with making false statements to Congress.
President Donald Trump welcomed the indictment against a high-profile figure who has long drawn his ire.
Mr Comey is accused of lying to a Senate committee in 2020 about whether he authorised a leak of classified information to the media.
The indictment in Virginia comes days after Trump called on the country's top law enforcement official to more aggressively investigate his political adversaries, including Mr Comey.
Mr Comey said he had "great confidence in the federal judicial system".
If found guilty, he could face up to five years in prison.
An indictment in the US justice system is a formal accusation issued by a grand jury after they review evidence to determine if a case should proceed.
Mr Comey's arraignment - where charges are formally read out in front of a defendant in court - has been set for 9 October in Alexandria, Virginia.
The probe is being led by Lindsey Halligan, the US Attorney for the Eastern District of Virginia, who was previously Trump's personal lawyer and took over her new role on Monday.
Attorney General Pam Bondi, urged by Trump at the weekend to pursue Mr Comey, said in a statement that the indictment "reflects this Department of Justice's commitment to holding those who abuse positions of power accountable for misleading the American people".
The two-page indictment is short on detail, but it says Mr Comey has been charged with one count of making false statements and another of obstruction of justice.
The five-year statute of limitations for charges would have expired next week.
The first count relates to Mr Comey telling the congressional committee he had not authorised someone else at the FBI to be an anonymous source in news reports about an FBI investigation into what the indictment describes as "PERSON 1", believed to be Clinton.
The political importance lies in whether the issue moves from public comment into formal action, party response, court record, election authority notice or administrative decision.
For public institutions and political groups, the next test is whether the issue remains a public argument or turns into a formal response, legal proceeding, administrative instruction or election-related communication.
