"What else is there? You know the answer. How many times has that question been asked," he said.
Flynn pleaded guilty Dec. 1 to lying to the FBI, making him the first Trump White House official to be charged with a crime in special counsel Robert Mueller's Russia probe.
Trump fired Flynn only 24 days into his tenure as national security advisor, saying at the time that the dismissal was a result of Flynn's false statements to Vice President Mike Pence.
Following Flynn's charge, however, a tweet sent from the president's account suggested that the president also knew at the time that Flynn had lied to FBI agents, which is a crime.
"I had to fire General Flynn because he lied to the Vice President and the FBI," the Dec. 2 tweet said.
Trump tweet: I had to fire General Flynn because he lied to the Vice President and the FBI. He has pled guilty to those lies. It is a shame because his actions during the transition were lawful. There was nothing to hide!
Trump lawyer John Dowd later said he was the author of the tweet.
If the president knew at the time that Flynn had committed a crime, it could raise questions about whether he obstructed justice, legal experts have said.
Dowd has said that a president cannot obstruct justice. He called that assertion "ignorant and arrogant."
The day after Flynn was fired, the president told FBI Director James Comey that he hoped he could "see your way clear to letting this go, to letting Flynn go," according to Comey's written testimony to Congress.
"I had understood the President to be requesting that we drop any investigation of Flynn in connection with false statements about his conversations with the Russian Ambassador in December," Comey wrote.