Malamud wrote slowly and carefully; he is the author of eight novels and four collections of short stories. The posthumously published Complete Stories contains 55 short stories and is 629 pages long. 

He completed his first novel, The Light Sleeper, in 1948, but later burned the manuscript. His first published novel was The Natural (1952), which has become one of his best remembered and most symbolic works. The story traces the life of Roy Hobbs, an unknown middle-aged baseball player who achieves legendary status with his stellar talent. This novel was made into a 1984 movie starring Robert Redford.

Malamud's second novel, The Assistant (1957), set in New York and drawing on Malamud's own childhood, is an account of the life of Morris Bober, a Jewish immigrant who owns a grocery store in Brooklyn. Although he is struggling financially, Bober takes in a drifter of dubious character. This novel was quickly followed by The Margic Barrel, his first published collection of short stories (1958). It won Malamud the first of two National Book Awards that he received in his lifetime.

In 1967, his novel The Fixer about anti-semetism in the Russian Empire, became one of the few books to receive the National Book Award for fiction and the Pulitzer Prize for fiction. His other novels include Dublin's Lives a powerful evocation of middle age (largely inspired by Malamud's own extramarital affairs) that employs biography to recreate the narrative richness of its protagonists' lives, and The Tenants perhaps a meta-narrative on Malamud's own writing and creative struggles, which, set in New York City deals with racial issues and the emergence of black/African American literature in the American 1970s landscape.

Malamud was renowned for his short stories, often oblique allegories set in a dreamlike urban ghetto of immigrant Jews. Of Malamud, Flannery O'Connor wrote: "I have discovered a short-story writer who is better than any of them, including myself." He published his first stories in 1943, "Benefit Performance" in Threshold and "The Place Is Different Now" in American Preface. Shortly after joining the faculty of Oregon State University, his stories began appearing in Harper's Bazaar, The New Yorker, Partisan Review, and Commentary.