The grandson of a Hungarian immigrant and the son of a court stenographer, Gould is reported to have developed his interest in biology as a five-year old when he first saw Tyrannosaurus rex at the American Museum of Natural History. Born in New York City, he was educated at Antioch University, Pennsylvania, and at Columbia, where he completed his PhD in 1967. He immediately moved to Harvard where he has served as professor of geology and curator of the Harvard Museum of Comparative Zoology since 1973.

Gould is widely known for eight volumes of essays on natural history published since 1978. The articles are usually about some aspect of evolution and are rooted firmly in history, carry a detailed argument, and are relevant to some contemporary issue. He has also published a number of influential monographs. In Ontogeny and Phylogeny (1977) he examined the notion of recapitulation – the view that individual development (ontogeny) is a rerun of evolutionary history (phylogeny). The Mismeasure of Man (1984) sought to demonstrate that attempts to measure man's intelligence were often designed to serve political rather than scientific ends. In a further monograph, Wonderful Life (1990) Gould has surveyed the fossils of the Burgess Shale, first described by C. D. Walcott. He used the fossils to illustrate a familiar theme of his work that evolution is not “a ladder of predictable progress,” it is rather “a copiously branching bush, continually pruned by the grim reaper of extinction.”

In the fields of paleontology and ecology Gould has worked for many years on the West Indian land snail, Cerion. As an evolutionary theorist he is best known for proposing in 1972, along with Nils Eldredge, the punctuated equilibrium hypothesis, which views evolution as episodic rather than continuous. Relatively short periods of branching speciation, they argued, are followed by much longer periods of stasis.

In 1981 Gould was very much in the news as one of the biologists called as an expert witness in the so-called Scopes II trial in Arkansas. Fundamentalists had claimed as equal a right to teach creationism in the Arkansas public schools as biology teachers had long claimed for Darwinism. Judge William Overton ruled in 1985 that creationism was a religious doctrine and it would therefore be a violation of the constitution if it were to be taught in public schools.