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WASHINGTON – Kathleen Sebelius, the health and human services secretary, is resigning, ending a stormy five-year tenure marred by the disastrous rollout of President Obama’s signature legislative achievement, the Affordable Care Act.

Obama accepted Sebelius’ resignation this week, and this morning he will nominate Sylvia Mathews Burwell, the director of the Office of Management and Budget, to replace her, officials said.

The departure comes as the Obama administration tries to move beyond its early stumbles in carrying out the law, persuade a still-skeptical public of its lasting benefits and help Democratic incumbents, who face attack ads after supporting the legislation, survive the midterm elections this fall.

Officials said Sebelius, 65, made the decision to resign and was not forced out. But the frustration at the White House over her performance had become increasingly clear, as administration aides worried that the crippling problems at HealthCare.gov, the website set up to enroll Americans in insurance exchanges, would result in lasting damage to the president’s legacy.

Even last week, as Obama triumphantly announced that enrollments in the exchanges had exceeded 7 million, Sebelius did not appear next to him for the news conference in the Rose Garden.

The president is hoping that Burwell, 48, a Harvard- and Oxford-educated West Virginia native with a background in economic policy, will bring an intense focus and management acumen to the department. The budget office, which she has overseen since April of last year, is deeply involved in developing and carrying out health care policy.

“The president wants to make sure we have a proven manager and relentless implementer in the job over there, which is why he is going to nominate Sylvia,” said Denis R. McDonough, the White House chief of staff.

Last month, Sebelius approached Obama and began a series of conversations about her future, McDonough said. The health secretary told the president that the March 31 deadline for sign-ups under the health care law – and rising enrollment numbers – provided an opportunity for change and that he would be best served by someone who was not the target of so much political ire, McDonough said.

“What was clear is that she thought that it was time to transition the leadership to somebody else,” he said. “She’s made clear in other comments publicly that she recognizes that she takes a lot of the incoming. She does hope – all of us hope – that we can get beyond the partisan sniping.”

The resignation is a low point in what had been a remarkable career for Sebelius, who as governor of Kansas was named by Time magazine as one of the five best governors in the country and was even mentioned as a possible running mate for Obama in 2008. The two had bonded when Sebelius endorsed his presidential bid early in 2008, becoming one of the highest-profile Democratic women to back him over Hillary Rodham Clinton and helping him deliver a big win in the Kansas caucus.

White House officials were quick to point out the many successes during Sebelius’ tenure: the end to pre-existing conditions as a bar to insurance, the ability for young people to stay on their parents’ insurance and the reduction in the growth of health care costs. In addition, Sebelius helped push through mental health parity in insurance plans and worked with the Department of Education to promote early childhood education.

Sebelius said in an interview Thursday that she always knew that she would not “be here to turn out the lights in 2017.”

“My balance has always been, when do you make that decision?” she added.

The president had been under pressure for months to fire Sebelius. But he had resisted, in part because he did not want the Department of Health and Human Services to undergo more upheaval amid all the problems plaguing HealthCare.gov and in part because of his general reluctance to publicly rebuke top officials.

In November, Obama defended the secretary, saying in an interview with NBC News that she “doesn’t write code; yeah, she wasn’t our IT person.”

McDonough on Thursday praised Sebelius as “a fierce advocate” and said she had been “tenacious in her belief” in the president’s health care law.

“She’s fearless in her defense of this idea at the heart of the Affordable Care Act,” he said. “The president has commented to me countless times how much he admires that.”

But the Affordable Care Act faces a range of obstacles, political and otherwise, in the months ahead, and Obama is hoping that Burwell can smoothly steer the department and bring stability to its operations. In addition to the midterm elections, in which the health care law is the target of a flood of negative ads, the administration is grappling with policy questions: how it will levy the penalty on individuals who lack insurance, how much will premiums increase in the coming year and how ultimately to administer the requirement that employers provide insurance.

In hearings on Capitol Hill, Sebelius sometimes grew rattled under grillings by lawmakers. In one hearing at the end of October, Sebelius declared that HealthCare.gov “has never crashed.”

“It is functional,” she added, “but at a very slow speed and very low reliability, and has continued to function.”

She made that statement even as large screens in the hearing room showed a live shot of the website with a page that said: “The system is down at the moment. We are experiencing technical difficulties and hope to have them resolved soon.”

An appearance on “The Daily Show With Jon Stewart” in October went even worse. Stewart challenged her to “sign up for Obamacare” before he could download every movie ever made.

“We’ll see which happens first,” he joked as she struggled to defend the website and the health care law.