A plea hearing has been set for 3.30pm GMT on Friday, the Office of the Special Counsel said.
It is alleged that Mr Flynn was dishonest about contacts with Russia's ambassador to the United States, Sergey Kislyak.
A court paper says that Mr Flynn "did wilfully and knowingly make materially false, fictitious, and fraudulent statements and representations".
It adds that Mr Flynn "falsely stated and represented to agents of the Federal Bureau of Investigation" his dealings with the Russian ambassador.
The charges relate to events late last year, during the transition period between President Obama and President Trump, when the United States imposed sanctions on Russia, and when a United Nations Security Council resolution was pending.
He was interviewed by the FBI just days after Mr Trump's inauguration on 20 January, and forced to resign in February after White House officials claimed he had misled them about whether he had had discussions with Mr Kislyak.
These latest events mean Mr Flynn has become the fourth person to be charged in an investigation led by special counsel Robert Mueller and a team of prosecutors.
Charges against three other Trump officials were announced last month.
They are: former campaign manager Paul Manafort, his business associate Rick Gates, and former foreign policy adviser George Papadopoulos.
More follows....