Dr. Rochelle Walensky, the director of the Centers for Disease Control and Prevention, will step down from her position on June 30, she announced on Friday, capping a tumultuous tenure at the nation’s leading public health agency as it struggled to rein in the Covid-19 pandemic, the greatest threat to American well-being in decades.

“She marshaled our finest scientists and public health experts to turn the tide on the urgent crises we’ve faced,” President Biden said in a statement after the announcement. “Dr. Walensky leaves C.D.C. a stronger institution, better positioned to confront health threats and protect Americans.”

In an agencywide meeting, Dr. Walensky admitted to having mixed emotions about her decision and broke down in tears, according to people on a conference call with her.

“I took on this role with the goal of leaving behind the dark days of the pandemic and moving the C.D.C. — and public health — into a much better and more trusted place,” she said in a subsequent email to agency staff.

During her tenure, Dr. Walensky noted, the agency administered more than 670 million Covid vaccine doses and provided guidance on immunization, social distancing and masking that “protected the country and the world from the greatest infectious disease threat we have seen in over 100 years.”

Her announcement came on the heels of the agency’s disclosure that it would dramatically scale back its surveillance of Covid. The Biden administration plans to end the public health emergency on May 11.

Dr. Walensky did not respond to a request for comment.

It was not immediately clear who would lead the C.D.C. after Dr. Walensky’s departure. Public health experts said the news came as a surprise, and some expressed disappointment in her decision.

“I think it is a loss for the C.D.C. and for the nation,” said Dr. Megan Ranney, the deputy dean for Brown University’s School of Public Health. “I know that it has not been easy, not just because of Covid but because of the politicization of science.”

With her resignation, Dr. Walensky joins the ranks of many other public health officials who left their jobs after the pandemic began, many of them because of harassment from the public.

Dr. Ranney said she received hate mail and personal attacks, but what she has experienced is “only the tip of the iceberg” compared with how Dr. Walensky has been treated.

A person familiar with Dr. Walensky’s thinking said that she had wearied of a barrage of harassment and long commutes between the C.D.C.’s offices in Atlanta and her home in Massachusetts. The director was upset by the agency’s relations with the White House and did not expect the announcement of the end of the public health emergency, the person said.

Born Rochelle Bersoff, Dr. Walensky grew up in Potomac, Md., in a family of respected scientists. She trained in medicine at Johns Hopkins University and, in 2001, joined the faculty at Harvard, where she developed a reputation as a rigorous researcher and a generous mentor.

Before her tenure as C.D.C. director, Dr. Walensky led the infectious diseases division at Massachusetts General Hospital, where she saw the pandemic’s devastation firsthand. She was noted for her work on health care policy, particularly in H.I.V.

But with little experience working in government and leading large institutions, Dr. Walensky was an unexpected choice to guide an agency with a staff of about 11,000 people.

Dr. Walensky took the helm of the beleaguered agency in January 2021. She had a near-impossible task ahead of her: restoring the reputation of the once-storied C.D.C. when public trust in the agency, and science more broadly, was fast ebbing.

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 and meddled with or ignored its research reports, undermining the morale of scientists even as the crisis ballooned.

Dr. Anthony S. Fauci, the nation’s leading adviser on Covid until late last year, told The New York Times in 2021 that he had full faith in Dr. Walensky’s ability to turn the C.D.C. around. “By the end of one year, everybody’s going to be raving about her,” he said at the time. “I guarantee it.”

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 face 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 commercial interests outweigh scientific caution.

Republicans in Congress repeatedly asked for her resignation and painted the agency as a failed institution in hearings on the pandemic. But some experts felt Dr. Walensky had done her best with an impossible hand.

“Dr. Walensky landed in this role during the height of Covid and gave it her all,” said Dr. Tom Inglesby, who worked with her closely when he served as the White House’s testing coordinator last year. “She has been working hard to change C.D.C. for the better, to evolve its structures and organization into one that can deal with the crises of the future. She will be sorely missed.”

Dr. Daniel Pollock, who led Covid surveillance for a few months in 2020 and retired in 2021 after 37 years at the agency, said: “This is a sad day for Rochelle Walensky and for C.D.C. So much is at stake as C.D.C. seeks to reorganize and modernize.”

“The timing of this leadership transition is very problematic,” he said. “I worked at C.D.C. under 10 different directors, and when they leave abruptly, for whatever reason, the ripple effects take a big toll.”

Despite the controversy, Dr. Walensky’s email to staff on Friday suggested that she believed she had improved the agency’s standing. “We collectively moved C.D.C. forward, reorganizing the agency and embarking on the necessary work to orient the enterprise toward public health action and foster accountability, timeliness and transparency in our work,” she said.

Dr. Walensky acknowledged the agency’s failings last year and promised to reorganize it, transforming its ability to respond quickly to public health crises. Some organizational changes have been announced, but it is unclear whether any of them have made a material difference in the C.D.C.’s work.

Under her leadership, Dr. Walensky said in her email to staff members, the agency bolstered its public health infrastructure and secured hundreds of millions of dollars to modernize the country’s data infrastructure.

She also declared racism a serious public health threat, she noted, and led the agency in its efforts to contain a multinational mpox outbreak, as well as the spread of Ebola in Uganda.

“We made this world a safer place,” Dr. Walensky said. “I have never been prouder of anything I have done in my professional career.”

Noah Weiland contributed reporting.

This is a developing story. Please check back for updates.