Retired Army Lieutenant General Flynn twice pleaded guilty to lying to the FBI during the last presidential transition in late 2016 about his phone calls to a Russian diplomat. Flynn urged the Russian ambassador in the talks not to escalate in reaction to the Obama administration putting sanctions on Russia over interference with the election.
Information of the call emerged as part of a larger inquiry into Russia's involvement in the US elections of 2016.
The move on Flynn's conviction will be part of a series of pardons expected by Mr. Trump before he leaves office on 20 January, some of the final exercises of his executive powers.
Back in March, Mr. Trump said that he was considering Flynn's full pardon, claiming the FBI and Justice Department had "destroyed" the life of the retired general.
He also tweeted that Flynn was an innocent man" who was a victim of officials in the Obama administration.
"What happened to the war hero, General Michael Flynn, should never be allowed to happen again to a U.S. resident!" In April, Mr. Trump said.
The prosecution against Flynn started in 2016 and he was convicted after pleading guilty in the investigation of Moscow's involvement in the US election in favor of Mr. Trump by former Special Counsel Robert Mueller.
Flynn later, however, tried to retract his assertion, demanding a withdrawal of his guilty plea last year, saying he never lied to investigators. The case was pending as Flynn is awaiting the decision of Judge Sullivan to remove his charges from the Justice Department.
As the time for Mr. Trump to leave the White House arrives, Democrats and legal experts worry that he will use his influence to benefit members of the family, personal ties, and even forgive himself.