In announcing his decision, Trump posted online that Dr Means "has impeccable 'MAHA' credentials" and will "reverse the Chronic Disease Epidemic".
The president said Dr Nesheiwat would work in another unspecified position in the health department.
Dr Means, 37, received a medical degree from Stanford University but later dropped out of a medical residency programme. She co-founded Levels, a glucose monitoring company, and according to her website, held research positions at the National Institutes of Health and several universities.
In 2024, she co-wrote a book with her brother Calley Means called Good Energy: The Surprising Connection Between Metabolism and Limitless Health.
The book drew attention from a range of conservative podcasters including Joe Rogan and Tucker Carlson.
On Mr Carlson' s podcast, she said chronic illnesses are "driven by our toxic food system and our toxic environment.
"These subtle insidious forces which are creating slow progressive illness… allow patients to be profitable and on the pharma treadmill for their entire lives," she said. "They make us sick but they don't kill us, but we are drugged for life."
The siblings are strong supporters of Secretary Kennedy, and in a celebratory post after his swearing in, Dr Means said RFK Jr "has a vision for the future that aligns with what I want for my family, future children, and the world."
A confirmation hearing for Dr Nesheiwat's nomination was scheduled for Thursday, but last month a report surfaced that she misrepresented her medical degree