Kendall, a dentist's son from South Norwalk, Connecticut, studied chemistry at Columbia University where he obtained his PhD in 1910. After working briefly at St. Luke's Hospital in New York from 1911 to 1914, Kendall moved to the Mayo Foundation in Rochester, Minnesota, where from 1921 to 1951 he served as professor of physiological chemistry.

In 1914 Kendall achieved an early success by isolating the active constituent of the thyroid gland. The importance of hormones in the physiology of the body had become apparent through the work of William Bayliss and Ernest Starling on the pancreas. Kendall was able to demonstrate the presence of a physiologically active compound of the amino acid tyrosine and iodine, which he named thyroxin.

Kendall was led from this to investigate the more complex activity of the adrenal gland. This gland secretes a large number of steroids, many of which he succeeded in isolating. Four compounds, labeled A, B, E, and F, seemed to possess significant physiological activity. They were shown to affect the metabolism of proteins and carbohydrates and in their absence animals seemed to lose the ability to deal with toxic substances. It was therefore hoped that some of these compounds might turn out to be therapeutically useful. After much effort sufficient compound A was obtained but, to Kendall's surprise and disappointment, it was shown to have little effect on Addison's disease, a complaint caused by a deficient secretion from the adrenal cortex. Kendall was more successful with his compound E – later known as cortisone to avoid confusion with vitamin E – when in 1947 a practical method for its production was established. Clinical trials showed it to be effective against rheumatoid arthritis. It was for this work that Kendall shared the 1950 Nobel Prize for physiology or medicine with Tadeus Reichstein and Philip Hench.