Born in Liverpool, Elton graduated in zoology from Oxford University in 1922. He was assistant to Julian Huxley on the Oxford University expedition to Spitzbergen (1921), where Elton carried out ecological studies of the region's animal life. Further Arctic expeditions were made in 1923, 1924, and 1930. Such experience prompted his appointment as biological consultant to the Hudson's Bay Company, for which he carried out investigations into variations in the numbers of fur-bearing animals, using trapper's records dating back to 1736. In 1932 Elton helped establish the Bureau of Animal Population at Oxford – an institution that subsequently became an international center for information on and research into animal numbers and their ecology. In the same year he became editor of the new Journal of Animal Ecology, launched by the British Ecological Society, and in 1936 was appointed reader in animal ecology as well as a senior research fellow by Oxford University.

Elton was one of the first biologists to study animals in relation to their environment and other animals and plants. His demonstration of the nature of food chains and cycles, as well as such topics as the reasons for differences in animal numbers, were discussed in Animal Ecology (1927). In 1930 Animal Ecology and Evolution was published in which he advanced the notion that animals were not invariably at the mercy of their environment but commonly, perhaps through migration, practiced environmental selection by changing their habitats. Work on the rodent population of Britain, and how it is affected by a changing environment, was turned to eminently practical account at the outbreak of World War II when Elton conducted intensive research into methods of controlling rats and mice and thus conserving food for the war effort. Voles, Mice and Lemmings: Problems in Population Dynamics was published in 1942, and The Control of Rats and Mice in 1954, the latter becoming accepted as the standard work on the subject.