The president says his former national security adviser's life had been "destroyed" because of the lie.
"I feel badly for General Flynn. I feel very badly. He's led a very strong life, and I feel very badly," Trump told reporters as he boarded Marine One on his way to Utah.
Trump pointedly ignored questions about exactly when he learned that Flynn had lied to FBI agents in January about conversations Flynn had with then-Russian Ambassador Sergey Kislyak. Instead, the president pivoted to attacking Hillary Clinton, his Democratic rival in the 2016 election.
"I will say this, Hillary Clinton lied many times to the FBI. Nothing happened to her. Flynn lied and they destroyed his life. I think it's a shame," Trump said.
"Hillary Clinton, on the Fourth of July weekend, went to the FBI, not under oath. It was the most incredible thing anyone's ever seen. She lied many times; nothing happened to her. Flynn lied, and they ruined his life. It's very unfair."
Trump was referring to a July 2, 2016, interview the FBI conducted with Clinton about her use of a private email server. According to the FBI, Clinton said repeatedly in the interview that she couldn't recall key details about the handling of classified materials.
Flynn pleaded guilty on Friday to one count of lying to the FBI, making him the fourth former Trump campaign official to face charges in the ongoing special counsel Robert Mueller's investigation into Russian meddling in the election.
In his plea, Flynn described how he was directed to contact Kislyak to request that Russia issue a muted response to new Obama administration sanctions announced last December for suspected election meddling. Flynn also said he was directed to contact Russian officials, as well as officials from other nations, to urge them to delay or postpone a vote on a U.N. resolution condemning Israel's continued building of settlements in the occupied West Bank.