President-elect Donald J. Trump said on Tuesday evening that he had selected Dr. Jay Bhattacharya, a Stanford physician and economist whose authorship of an anti-lockdown treatise during the coronavirus pandemic made him a central figure in a bitter public health debate, to be the director of the National Institutes of Health.

“Together, Jay and RFK Jr. will restore the NIH to a Gold Standard of Medical Research as they examine the underlying causes of, and solutions to, America’s biggest health challenges, including our Crisis of Chronic Illness and Disease,” Mr. Trump wrote on social media, referring to Robert F. Kennedy Jr., his choice to lead the N.I.H.’s parent agency, the Department of Health and Human Services.

If confirmed by the Senate, Dr. Bhattacharya would lead the world’s premier medical research agency, with a $48 billion budget and 27 separate institutes and centers, each with its own research agenda, focusing on different diseases like cancer and diabetes. Dr. Bhattacharya, who is not a practicing physician, has called for overhauling the N.I.H. and limiting the power of civil servants who, he believes, played too prominent a role in shaping federal policy during the pandemic.

He is the latest in a series of Trump health picks who came to prominence during the coronavirus pandemic and who hold views on medicine and public health that are at times outside the mainstream. The president-elect’s health choices, experts agree, suggest a shake-up is coming to the nation’s public health and biomedical establishment.

Dr. Bhattacharya is one of three lead authors of the Great Barrington Declaration, a manifesto issued in 2020 that contended that the virus should be allowed to spread among young healthy people who were “at minimal risk of death” and could thus develop natural immunity, while prevention efforts were targeted to older people and the vulnerable.

Through a connection with a Stanford colleague, Dr. Scott Atlas, who was advising Mr. Trump during his first term, Dr. Bhattacharya presented his views to Alex M. Azar II, Mr. Trump’s health secretary. The condemnation from the public health establishment was swift. Dr. Bhattacharya and his fellow authors were promptly dismissed as cranks whose “fringe” policy prescriptions would lead to millions of unnecessary deaths.

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