Lewis was educated at the University of Minnesota, and at the California Institute of Technology gaining his PhD in 1942. In 1946 he joined the Cal Tech faculty, where he served as Professor of Biology from 1956 until his retirement in 1988.

Lewis has worked mainly in the field of developmental biology concentrating on the manner in which genes control the development of the fruit fly Drosophila melanogaster. In 1894, William Bateson described a characteristic set of mutations, named by him “homeotic mutations,” in which one body structure is replaced by a different structure. For example, an insect leg may be replaced by an insect wing. In the late 1940s, Lewis began to study a group of genes known as the bithorax complex, which control the manner in which Drosophila embryos become segmented as they develop. After decades spent breeding numerous generations of fruit flies Lewis finally published his main results in 1978.

Drosophila is divided into one head, three thoracic, and eight abdominal segments. The development of the head and first thoracic segment are controlled by the antennapedia complex; the remaining segments by the bithorax complex. Lewis found that a minimum of eight genes, clustered on chromosome 3, were involved in the segmentation of the fly's abdomen and thorax. Lewis demonstrated that the production of the second thoracic segment, which is the first to be controlled by the bithorax complex, was controlled by the fewest homeotic genes. Each later segment required the activation of one or more additional genes. The sequence of genes along the chromosome exactly matched the segments of the insect's body.

He also realized that a single mutation could lead to major homeotic transformations even though, for example, hundreds of active genes would be required to create misplaced legs and wings. This could only mean that mutations were also taking place in a master gene of some kind, a gene capable of controlling the activity of many other subordinate genes.

For his work on homeotic genes Lewis shared the 1995 Nobel Prize for physiology or medicine with Eric Wieschaus and Christiane Nüsslein-Volhard.