Born at Oakland in California, Miller was educated at the universities of California and Chicago where, in 1954, he was awarded his PhD. From 1960 he taught at the University of California, San Diego, being appointed to a professorship in chemistry in 1968.

In 1953 Miller published a famous paper, A Production of Amino Acids under Possible Primitive Earth Conditions, in which he reported the results of an experiment carried out while still a graduate student at Chicago under the direction of Harold Urey.

It was thought that the early atmosphere of the Earth could well have been something like that now existing on Jupiter and Saturn, namely one rich in methane (CH₄) and ammonia (NH₃). Miller mixed water vapor with ammonia, methane, and hydrogen in a closed flask and subjected it to a high-voltage electrical discharge. Sensitive analysis with paper chromatography revealed a number of organic molecules. In addition to hydrocyanic acid, formic acid, acetic acid, lactic acid, and urea were two of the simpler amino acids, alanine and glycine.

As it is from the amino acids that the proteins are constructed many scholars saw this as clear evidence for the spontaneous origin of life. It has however been shown that such random processes could not yet have produced a single protein without the assumption of various additional operating principles.