Whipple began work at the Harvard College Observatory in 1931 and, during World War II, came up with the idea of dropping aluminum foil strips from aircraft to confuse German radar.
In 1950 he revolutionized the study of comets when he proposed they were not "sandbags," but small bodies made of rock, dust and ice, or, as he put it, comets were "dirty snowballs."
"This was a complete paradigm switch since, back then, the consensus model for a comet was a flying cloud of particles," Don Yeomans, of the U.S. Jet Propulsion Laboratory in California told the BBC.
Whipple discovered six comets, all of which were named for him, the BBC said. He also predicted the advent of artificial satellites and had already prepared a satellite tracking network when the first satellite, Sputnik, was launched by the Soviet Union in 1957.
He was the first to compute an accurate orbit for the then recently discovered Pluto and also made important contributions in such fields as astronomical instrumentation, radio astronomy, and the study of variable stars, galaxies, stellar evolution and supernovas, the BBC said.
From 1955 to 1973 he directed the Smithsonian Astrophysical Observatory, which is now the renowned Harvard Smithsonian Center for Astrophysics.
"Fred was one of the truly great forces in astronomical research, and our field has gained immeasurably as a result of his insights," said Yeomans.