Whipple, born the son of a physician in Ashland, New Hampshire, was educated at Yale and Johns Hopkins University, where he obtained his MD in 1905. After working at the University of California he moved in 1921 to the University of Rochester, where he served as professor of pathology until his retirement in 1955.

Whipple began his research career by working on bile pigments but went on to study the formation and breakdown of the blood pigment, hemoglobin, of which bile pigments are the breakdown products. To do this he bled dogs until he had reduced their hemoglobin level to a third, then measured the rate of hemoglobin regeneration. He soon noted that this rate varied with the diet of the dogs and by 1923 reported that liver in the diet produced a significant increase in hemoglobin production.

It was this work that led George Minot (1885–1950) and William Murphy (1892–1987) to develop a successful treatment for pernicious anemia and earned all three men the Nobel Prize for physiology or medicine in 1934.