The National Institutes of Health, the world’s leading public funder of biomedical research, has an enviable track record. Research supported by the agency has led to more than 100 Nobel Prizes and has supported more than 99 percent of the drugs approved by federal regulators from 2010 to 2019.

No surprise, then, that the agency has been called “the crown jewel of the federal government.” But come January, when President-elect Donald J. Trump and congressional Republicans take charge, the N.I.H. may face a reckoning.

Robert F. Kennedy, Jr., the new administration’s selection for secretary of the Department of Health and Human Services, which oversees the N.I.H., routinely castigates federal scientists and is a staunch critic of conventional pharmaceuticals and vaccines, with a long record of spreading falsehoods about vaccine safety.

He has said that he would steer the agency into a yearslong “break” from infectious disease research, focusing instead on chronic diseases.

And Mr. Trump’s pick for N.I.H. director, Dr. Jay Bhattacharya, the Stanford professor who gained notoriety during the pandemic for supporting the widely maligned idea that the coronavirus should be left to spread freely among healthy Americans,has called for a dramatic restructuring of the N.I.H., which he has said is led by small-minded bureaucrats.

While even the agency’s defenders acknowledge that the N.I.H. needs modernization, the radical reforms now proposed would be difficult, if not impossible, without years of legal wrangling and significant support from Congress, experts say.