"It is my Great Honor to announce that General Michael T. Flynn has been granted a Full Pardon," Trump said on Twitter on Wednesday.
"Congratulations to @GenFlynn and his wonderful family, I know you will now have a truly fantastic Thanksgiving!"
A retired Army general, Flynn pleaded guilty in 2017 to lying to the FBI about interactions he had with Russia's ambassador to the United States in the weeks leading up to Trump's inauguration in January 2017.
He has since sought to withdraw the plea, arguing that prosecutors violated his rights and duped him into a plea agreement. His sentencing has been deferred several times.
It was the highest-profile pardon granted by Trump since he took office.
Among others, the Republican president has pardoned army personnel accused of war crimes in Afghanistan and Joe Arpaio, a former Arizona sheriff and hardliner against illegal immigration.
Flynn served as Trump's first national security adviser but the president fired him in early 2017 after only 24 days as a controversy broke over the former general's contacts with then Russian Ambassador Sergei Kislyak.
Flynn was one of several former Trump aides to plead guilty or be convicted at trial in former Special Counsel Robert Mueller's investigation into Moscow's interference in the 2016 US election to boost Trump's candidacy.
Russia denied meddling.
Trump in March said he was strongly considering a full pardon for Flynn.
He said the FBI and Justice Department had "destroyed" Flynn's life and that of his family, and cited an unspecified, unsubstantiated report that they had lost records related to Flynn.
Flynn was supposed to help co-operate with the government as part of his plea deal.
But he later switched lawyers and tactics, arguing prosecutors in the case had tricked him into lying about his December 2016 conversations with Kislyak.
The Justice Department has repeatedly denied allegations of prosecutorial misconduct and US District Court Judge Emmet Sullivan rejected all Flynn's claims in December 2019.
Federal prosecutors had asked the judge in January to sentence Flynn to up to six months in prison, arguing in a court filing that "the defendant has not learned his lesson. He has behaved as though the law does not apply to him, and as if there are no consequences for his actions."
Flynn also served as head of the Pentagon's Defense Intelligence Agency but was forced out in 2014 in part due to his management style and opinions on how to fight Islamist militancy.
He joined the Trump 2016 election campaign and at the Republican National Convention that year led supporters in chants of "Lock her up," in reference to Democratic candidate Hillary Clinton.