The C.D.C. had been pilloried since the start of the pandemic for missteps in testing, changing advice on masking, and antiquated surveillance and data systems. Trump administration officials hectored the agency’s leaders, rewrote its guidance and meddled with its research reports, undermining the morale of scientists even as the crisis ballooned.

“She insisted that people act more promptly and in a more focused way, so she stimulated people to do things perhaps a little bit differently than they had,” said Dr. William Schaffner, an infectious diseases physician at Vanderbilt University who works closely with the agency.

“Morale within the C.D.C. distinctly improved under her leadership,” he added.

But the pandemic proved to be rough ground even for someone as respected and well-liked as Dr. Walensky. She was roundly criticized by experts for advising people to stop wearing their masks just weeks before the Delta variant of the coronavirus pummeled the nation.

And after shortening isolation requirements even as the Omicron variant brought the country to a standstill, she was accused of letting economic interests outweigh scientific caution.

Anne Sosin, who studies health equity at Dartmouth, said that Dr. Walensky had sometimes taken the fall for Biden administration decisions, but that she also could have done more to level with the public about the rationales for those decisions.