The leading physician was said to have walked out of a meeting of the White House coronavirus task force this summer, and decided never to return again.
She told colleagues that she would side-step any meetings with Dr Atlas, a controversial White House adviser without any background in infectious diseases or public health.
Mr Trump appointed him to the coronavirus taskforce in August, after appearing on Fox News for several months to challenge lockdowns, masks and other preventative measures.
“I hate to use the term doctor shopping, but it almost feels like if this is what President Trump did until he found someone in the medical field that agrees with him,” said CNN’s Kate Bennett on the report.
Dr Atlas had suggested last week that masks did not work to control the coronavirus’s spread, in a Twitter post that was censored as misinformation.
He also previously said there was “zero reason to panic” when Mr Trump was hospitalised with Covid-19, and pushed a herd immunity approach to end the pandemic - in what experts predict would cause an exceptionally high death toll.
"I've known Debbie a long time," Dr Jerome Kim, the director general of the International Vaccine Institute, and a former colleague of Dr Birx, told CNN. "She really is completely driven by getting things done and being effective, and I think she's frustrated,”
“If she can't get it done in the White House, the way to do it is go into the field and use personal diplomacy to convince politicians there is a right way to do this and a right way to approach things, and the consequences of failure are significant," said Dr Kim.
Dr Birx has reportedly travelled more than 20,000 miles and visited 40 states since August, conducting meetings with local health officials to advise on how to combat the pandemic.