Trump insisted he and his campaign had not colluded with Moscow in the election, and shifted blame on the Justice Department and rival Hillary Clinton.
In a series of tweets, Trump said that "nothing happened" to Hillary who lied many times to the FBI while General Flynn lied to the agency and his life is destroyed.
"I recognize that the actions I acknowledged in court today were wrong, and, through my faith in God, I am working to set things right," Flynn said in a statement.
The 57-year-old Flynn was one of the most prominent military veterans to endorse Trump's campaign.
Flynn has been charged with lying to investigators over his discussions with his Russian contacts regarding US sanctions being imposed on Moscow during Obama's government.
Flynn was forced to resign as national security adviser in February after White House officials concluded that he had misled them about the nature of his contacts.
The Arizona Republican says, "We've seen this movie before."
Flynn resigned the day before the Feb. 14 meeting, after it was revealed he apparently had lied to his about the nature of his contacts with Russia's ambassador.
Flynn, a former Army lieutenant general and Defense Intelligence Agency chief, accepted cash for his work on behalf of foreign interests.