McMillan was born in Redondo Beach, California, on September 18, 1907, the son of Edwin Harbaugh McMillan and his wife Anna Marie McMillan née Mattison. He had a younger sister, Catherine Helen. His father was a physician, as was his father's twin brother, and three of his mother's brothers. On October 18, 1908, the family moved to Pasadena, California, where he attended McKinley Elementary School from 1913 to 1918, Grant School from 1918 to 1920, and then Pasadena High School, from which he graduated in 1924.
California Institute of Technology (Caltech) was only a mile from his home, and he attended some of the public lectures there. He entered Caltech in 1924. He did a research project with Linus Pauling as an undergraduate and received his Bachelor of Science degree in 1928 and his Master of Science degree in 1929, writing an unpublished thesis on "An improved method for the determination of the radium content of rocks". He then took his Doctor of Philosophy from Princeton University in 1933, writing his thesis on the "Deflection of a Beam of HCI Molecules in a Non-Homogeneous Electric Field" under the supervision of Edward Condon.