The Senate confirmed Robert F. Kennedy Jr. as Health and Human Services secretary, putting a longtime critic of processed foods, big agriculture, vaccines and the medical establishment in charge of the nation’s vast and powerful health system.

Every Democrat voted against Kennedy, while Sen. Mitch McConnell, a polio survivor who had criticized the nominee’s questioning of vaccines, was the lone Republican no vote.

Mr. Kennedy is expected to be sworn in on Thursday afternoon to 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.

The Consumer Brands Association, which represents makers of ultraprocessed foods, issued a pointed statement, reminding Mr. Kennedy that they are the nation’s largest manufacturing employer, and that they would like to see aspects of the status quo remain in place.

“The federal regulatory agencies within H.H.S. operate under a science and risk-based mandate, and it is critical that framework remains under the new administration,” said Sarah Gallo, the group’s senior vice president for federal affairs.