He was expected to plead guilty to one count of knowingly making "false, fictitious and fraudulent statements", reports said. Ahead of Friday morning's court session in Washington DC, two officials were quoted by Reuters news agency as saying he had turned himself in to the FBI.
The former aide is the most senior member of the Trump administration so far to have been indicted by the Mueller investigation.
In October, Mr Trump's former presidential campaign manager, Paul Manafort, was accused of conspiring to defraud the US in his dealings with Ukraine. It also emerged that another ex-aide, George Papadopoulos, had pleaded guilty to making false statements to FBI agents.
Flynn was widely thought to be exposed to more serious charges, and the emerging consensus is that this looks like an extremely good deal for him, with a few months in Club Martha the likely sentence. In return, then, he must have spilled a lot of beans. https://twitter.com/SethAbramson/status/936605815603105792
Updated to reflect guilty plea.