Born in Red Oak, Iowa, Whipple graduated from the University of California in Los Angeles in 1927 and obtained his PhD from Berkeley in 1931. He then moved to Harvard where he became professor of astronomy in 1945, Philips Professor of Astronomy in 1950, and director of the Smithsonian Astrophysical Observatory from 1955 until his retirement in 1973.

He described his research as centering on “physical processes in the evolution of the solar system” and produced in this field a much admired work, Earth, Moon and Planets (1941 and many subsequent editions).

Whipple is also well known for his work on comets. In 1950 he proposed an icy-nucleus model in which he described the nucleus of a comet as a ‘dirty snowball’, made from a mixture of water ice and dust, plus carbon dioxide, carbon monoxide, methane, and ammonia ices, and only becoming active when passing close to the Sun. The main advantage of this model is that it can account for such distinctive features of comets as their orbital motion. It had been long known that some comets, such as Encke's, persist in returning earlier than Newtonian theory would predict while others, such as Halley's, arrive over four days later than expected. Whipple proposed that solar radiation would cause the ices on the outside of the cometary nucleus to evaporate, leaving a thin insulating layer of dust particles, and that this would set up a delayed jet reaction. The radiation has the effect of pushing further out those comets that are rotating in the same direction as their orbit. This will increase their orbit and delay their return. The radiation will produce a drag force on those comets rotating counter to their orbit, causing them to drift in toward the Sun, reducing their period and thus hastening their return.

As there should be no preferred direction of rotation, Whipple predicted that about half the comets should appear to be retarded and half accelerated in their orbit, an effect since confirmed.