President-elect Donald J. Trump announced on Friday that he would nominate Dr. Martin A. Makary, a Johns Hopkins University surgeon with a contrarian streak, to be commissioner of the Food and Drug Administration.

In a post on social media, Mr. Trump said: “F.D.A. has lost the trust of Americans and lost sight of its primary goal as a regulator.” He said that Dr. Makary would work under Robert F. Kennedy Jr., the president-elect’s choice for the cabinet-level role as health secretary, to “properly evaluate harmful chemicals poisoning our nation’s food supply and drugs.”

“I am confident that Dr. Makary, having dedicated his career to high-quality, lower-cost care will restore the F.D.A. to the gold standard of scientific research and cut the bureaucratic red tape at the agency to make sure Americans get the medical cures and treatments they deserve,” Mr. Trump said in a statement.

Dr. Makary, 54, rose to prominence more than a decade ago as a critic of the medical establishment, speaking out about patient safety and working with hospitals to improve practices. He also gained attention during the pandemic, weighing in on herd immunity, vaccines and masks in 2021, roiling some doctors who were still contending with packed I.C.U.s and hundreds of deaths a week.

As F.D.A. commissioner, Dr. Makary would lead an agency that has come under considerable fire from Mr. Kennedy Jr., who would be his boss if confirmed by the Senate to become secretary of the Department of Health and Human Services.

Mr. Kennedy has been outspoken in his desire to overhaul the F.D.A., saying he would fire agency staff members whom he argued had “suppressed” disputed and sometimes harmful treatments; would gut an entire department; and would clamp down on the food and pharmaceutical industries. Mr. Kennedy has also criticized the so-called user fees from drug and medical device companies that pay for thousands of employees to review industry products and account for nearly half of the agency’s overall budget of $7.2 billion.

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