Whitaker graduated from Dartmouth College in 1966 and earned his M.D. from Emory University School of Medicine in 1970, completing a surgical internship at Atlanta's Grady Memorial Hospital in 1971. He did postgraduate training at Emory University and began but did not complete a residency in orthopedic surgery at the University of California San Francisco.

He is "board certified" in "anti-aging medicine" by the American Board of Anti-Aging & Regenerative Medicine, an educational and certification program of the American Academy of Anti-Aging Medicine (A4M).

Whitaker suggests, in his subscription-based newsletter called Health and Healing and in numerous books, that a combination of vitamin therapy and exercise can prevent or cure many ailments. As the director and founder of the Whitaker Wellness Institute in Newport Beach, California, Whitaker states that since 1991, his subscription-based newsletter has achieved a circulation of more than 2.5 million readers. He is a co-founder of the California Orthomolecular Medical Society.

Whitaker opposes the use of pharmaceuticals in the treatment of mental illness and supports the Scientologist position, popularised by actor Tom Cruise, that psychiatry is fraudulent. In a CNN interview with Anderson Cooper, Whitaker states that psychiatric diagnoses have "no basis" and are fabricated or voted into existence by powerful groups of doctors with financial interests. The combination of medication and talk therapy endorsed by psychiatry is a "script", says Whitaker, who claims in the interview that his golden retriever can provide talk therapy just as well as a psychiatrist. According to Whitaker, vitamins, such as those promoted on his website, can cure psychiatric disorders by improving general health.

Whitaker has been a controversial figure, and has been criticized for his self-promotional approach to medicine, potential conflicts of interest, and his embrace of scientifically unsound practices.

The National Council Against Health Fraud (NCAHF) criticises Whitaker for promoting himself as "America's #1 health advocate," "America's #1 health champion," and "the physician America trusts." According to the NCAHF, Whitaker advocates potentially dangerous therapies involving growth hormones, chelation and megavitamins, and intervenes on behalf of other "maverick" doctors in legal trouble.

The Los Angeles Times notes that Whitaker serves as a consultant to vitamin companies advertised on his website, a practice criticised by other doctors who prefer to promote only evidence-based products. In the article, Whitaker is classified as a doctor "mixing celebrity and cyberspace".

Whitaker claims to be a leading expert in "anti-aging medicine", a practice criticised by mainstream medical practitioners.