The president attacked Dr Fauci on a campaign call to staffers and said that if the scientist had been in charge more than 500,000 Americans would have died.
“Fauci is a disaster. If I listened to him, we’d have 500,000 deaths,” Mr Trump said on the call, according to CNN.
“If there’s a reporter on, you can have it just the way I said it, I couldn’t care less.”
Mr Trump later in the call said there would have been between 700,000 and 800,000 deaths as he mocked Dr Fauci for having been around for “500 years.”
"People are tired of Covid. I have these huge rallies," Trump said.
"People are saying whatever. Just leave us alone. They're tired of it. People are tired of hearing Fauci and all these idiots - Fauci is a nice guy. He's been here for 500 years.”
The president’s attacks on Dr Fauci come after the scientist said he was “not surprised” that Mr Trump had come down with the virus.
Mr Trump also likened Dr Fauci’s TV appearances to discuss coronavirus as a “bomb” but said it was a “bigger bomb if you fire him.”
More than 224,000 Americans have died from coronavirus and 8.3 million have tested positive for it since the pandemic began.
Mr Trump was hospitalised for three days or treatment after testing positive for Covid-19, along with wife Melania and son Barron, and a number of his White House inner circle.
On the call the president also denied that there was tension between him and his White House chief of staff Mark Meadows, and he disputed reports he was planning on firing Mr Meadows after the election.
"I love Mark Meadows. It took me two years to get him out of Congress. Mark Meadows is doing a good job. I'm not dismissing him,” said Mr Trump.