Robert F. Kennedy Jr., the vaccine skeptic and former presidential candidate who fled his family’s party and threw his “medical freedom” movement behind President Trump, was confirmed by the Senate on Thursday as the nation’s next health secretary. He is expected to be sworn in at the White House by President Trump on Thursday afternoon.

The vote, 52 to 48, capped a remarkable rise for Mr. Kennedy and a curious twist in American politics. He was confirmed by a Republican Senate, without a single Democratic vote, in a chamber where his father, Robert F. Kennedy, and his uncles, John F. Kennedy and Edward M. Kennedy, all held office as Democrats.

Senator Mitch McConnell of Kentucky, a polio survivor and the former Republican leader, voted no, the lone Republican to oppose Mr. Kennedy. Mr. McConnell issued a searing statement explaining his vote.

“Individuals, parents and families have a right to push for a healthier nation and demand the best possible scientific guidance on preventing and treating illness,” it read in part. “But a record of trafficking in dangerous conspiracy theories and eroding trust in public health institutions does not entitle Mr. Kennedy to lead these important efforts.”

Mr. Kennedy will now lead the federal Department of Health and Human Services, a sprawling agency with 13 operating divisions, including some — the Food and Drug Administration, the National Institutes of Health and the Centers for Disease Control and Prevention — that he has called corrupt.

Those scientific agencies are already reeling from the onslaught of directives coming from the Trump administration. The N.I.H., targeted for budget cuts, has just lost its No. 2 official, who retired to avoid being pushed into a job he did not want, according to people familiar with his decision.

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