Born in Redonda Beach, California, McMillan was educated at the California Institute of Technology and at Princeton, where he obtained his PhD in 1932. He took up an appointment at the University of California at Berkeley in 1935, being made professor of physics in 1946 and director of the Lawrence Radiation Laboratory in 1958, posts he held until his retirement in 1973.

In 1940 McMillan and Philip Abelson announced the discovery of the first element heavier than uranium. The new element had a mass number 93 and a relative atomic mass of 239. It was named neptunium after the planet Neptune, just as 150 years earlier Martin Klaproth had named uranium after the planet Uranus. McMillan also suspected the existence of element 94 and in the same year was proved right by the discovery of the new element (plutonium) by Glenn Seaborg with whom he was to share the 1951 Nobel Prize for chemistry. The new elements were produced when uranium was bombarded with neutrons and were detected by virtue of their characteristic half-life.

McMillan also made a major advance in the development of Ernest Lawrence's cyclotron, which, in the early 1940s, had run up against a theoretical limit. Lawrence found that as his particles accelerated beyond a certain point their increase in mass, as predicted by Einstein's theory of relativity, was putting them out of phase with the electric impulse they were supposed to receive inside the cyclotron.

In 1945 McMillan proposed a neat solution in the synchrocyclotron (also independently suggested by Vladimir Veksler) in which the fixed frequency of the cyclotron was abandoned. The variable frequency of the synchrocyclotron could thus be adjusted to correspond to the relativistic mass gain of the accelerating particles and once more get into phase with them. In this way accelerators could be built that were forty times more powerful than Lawrence's most advanced cyclotron.