The Office of the Special Counsel said Flynn was charged with making false statements about his contacts with Russia`s ambassador to the United States.
The office, which is investigating accusations of Russian meddling in the 2016 U.S. presidential election and potential collusion by Trump`s campaign, said a plea hearing for Flynn had been set for Friday.
Flynn, a retired Army general, was expected to plead guilty.
He arrived at a court in downtown Washington on Friday morning.
Lawyers for Flynn could not be immediately reached for comment, Reuters reported.
Flynn, who was fired from his White House post in February for misleading Vice President Mike Pence about his conversations with the Russian ambassador, is a central figure in the investigation led by Special Counsel Robert Mueller.
He is the second former senior aide to Trump to be charged in the probe. Mueller`s investigation and several congressional probes into the matter have dogged Trump`s administration since the Republican president took office on Jan. 20.
Paul Manafort, who ran Trump`s presidential campaign for several months last year, was charged in October with conspiring to launder money, conspiracy against the United States and failing to register as a foreign agent of Ukraine's former pro-Russian government.
Manafort, who did not serve in Trump`s administration, and a business associate who was charged with him, pleaded not guilty.