It is certain to outrage Democrats and those who feel that Trump is preparing a long list of such pardons to give immunity to his family and loyalists.
But Trump's move will delight those on the American right who feel the 3-star General was a victim of a set-up by the President's political enemies.
Flynn admitted lying twice to the FBI and was initially convicted. But his trial has since become a legal quagmire as the Department of Justice changed its mind about whether he should have been prosecuted at all.
The Presidential pardon ends the whole controversial saga of a phone call that Flynn made to the Russian Ambassador, Sergei Kislyak, in late 2016.
It formed part of Democrats' accusations that Trump and his team were acting inappropriately towards an adversary.
The President saw the prosecution of Flynn as part of what he repeatedly called the "Russia Hoax." Now this is political payback - and a sign of gratitude to Flynn for his continuing loyalty.
Trump has already commuted the sentence of Roger Stone, another close associate.
It now raises the ultimate legal question: Will Trump try and pardon himself in a move designed to pre-empt any prosecution after he leaves office on January 20th?
Some experts already see Flynn’s likely pardon as a test case for the much bigger issue.
It’s the sort of issue that lawyers love to debate. Can a president pardon himself? If not, could he step aside for a day (under the 25th Amendment), get an acting President to issue a pardon, and then resume office?
The point is not entirely theoretical. Donald Trump loses much of his legal protection at noon on January 20th. Once he is no longer president, he is far more exposed to being charged with criminal misconduct.
In Trump’s case he could be investigated on charges of tax fraud. Court documents in New York indicate the Trump Organisation is being probed for "possibly extensive and protracted criminal conduct,” which could include falsifying business records and insurance fraud.
It is also possible that investigators might uncover other crimes related to corruption or nepotism.
But most lawyers believe that the Supreme Court - even a conservative one - would never let a President pardon himself. That would be an admission that one man is above the law - the President. And America fought a revolutionary war against that concept.
In any case, a presidential pardon would protect Trump only against federal charges. He could still be prosecuted for state crimes.
Alongside the political theatre of Trump’s non-concession is the parallel drama of the President’s legal battles. And those are only just beginning.