Trump made the announcement in a tweet Wednesday afternoon, ending the three-year legal saga that saw Flynn twice plead guilty to lying to the FBI during its investigation into Russian interference in the 2016 presidential election and later rescind the plea.
"It is my great honor to announce that General Michael T. Flynn has been granted a full pardon," Trump wrote. "Congratulations to @GenFlynn and his wonderful family, I know you will now have a truly fantastic Thanksgiving!"
Trump had said he was "strongly considering" granting Flynn a pardon as early as March, suggesting that the FBI and Justice Department lost some of Flynn's records related to his charge of making a false statement to the FBI.
He made those statements as part of former special counsel Robert Mueller's investigation into Russian meddling in the 2016 presidential election.
Flynn originally pleaded guilty to lying to the FBI about his contacts with former Russian ambassador Sergey Kislyak, but withdrew the guilty plea Jan. 14, stating prosecutors broke an agreement for his cooperation when they requested he receive jail time instead of probation.
His sentencing hearing then was indefinitely suspended in February, after his lawyers said the prosecution was unable to produce an internal Justice Department memo clearing Flynn of being a Russian agent.
Trump's full pardon comes as the transition of power to President-elect Joe Biden has begun, with the General Services Administration releasing transition funds to Biden's campaign and Trump signing off to allow Biden to receive the President's Daily Brief.