Flynn, 61, admitted to providing inaccurate information to the US’ Justice Department on his work relating to Turkey in 2017.
He also pleaded guilty to a single felony count of making false statements to the FBI about his Russian contacts.
The former national security adviser’s pardon has been seen as a culmination of a four-year saga from an FBI investigation into alleged co-operation between the Russian government and Trump during his 2016 presidential campaign.
“It is my Great Honour to announce that General Michael T Flynn has been granted a Full Pardon,” Trump announced on Twitter. “Congratulations to @GenFlynn and his wonderful family, I know you will now have a truly fantastic Thanksgiving!”
Flynn allegedly received a $15 million proposal to forcibly remove a Muslim cleric living in the US and return him to Turkey, the Wall Street Journal (WSJ) reported in 2017.
The cleric, Fethullah Gülen, is seen by Turkish President Recep Tayyip Erdogan as a political dissident who orchestrated the July 2016 coup attempt.
Flynn was involved in a December 2016 meeting held in New York with representatives of the Turkish government to discuss the extra-judicial extradition of Gülen, the WSJ report added.
During the meeting, Flynn reportedly entertained the possibility of transporting Gülen from the US to the Turkish prison island of Imrali on a private jet.
He was also involved in discussions to illegally extradite the Turkish cleric from the US as early as September 2016.
The former national security adviser was also paid more than $500,000 to spearhead a campaign to lobby for Turkish interests during the 2016 presidential election campaign.
In an Op-ed published by the Hill on election day in 2016, Flynn called on the US to be more sympathetic to Turkish needs while seemingly supporting Erdogan’s argument that Gülen was behind the failed coup attempt of that year.
Democrats have denounced the pardon, with Democratic Speaker of the House of Representatives Nancy Pelosi terming the decision “an act of grave corruption and a brazen abuse of power”, the Times reported.