Thompson was born in Saint Paul, Minnesota, graduated from Yale University in 1941, then spent four years in the United States Navy fighting in World War II. After the war he moved to Cambridge, Massachusetts where he spent the rest of his life.
Thompson began his career as an architect in 1946 when he convinced Walter Gropius to form The Architects' Collaborative with himself and four Yale classmates. In 1953 he founded Design Research, a company that provided interior furnishings and accessories. Design Research is often noted today for being the first U.S. proprietor of the Finnish clothing and textiles of Marimekko. Jaqueline Kennedy was pictured on the cover of Life Magazine in the early 60's in a Marimekko dress purchased at Thompson's Brattle Street store, boosting the fashion craze for the Finnish designs.
He also designed the company's first store, notable for its extreme openness and use of glass; the firm eventually added stores in New York (1964) and San Francisco (1965). Thomson's interest in modernism, however, was balanced by appreciation of older architecture. In the late 1950s he renovated Harvard Yard's historic dormitories by updating their interior arrangements without visible exterior effect. Shortly thereafter he persuaded Harvard to remodel Boylston Hall (built 1857) rather than demolish it.
During those years, Thompson taught architecture at Harvard University, and served as Department Chairman 1964-1968. His 1966 essay, “Visual Squalor and Social Disorder,” argued for an urban architecture that would encourage, rather than discourage, joy and social life. To this end, in 1967 he proposed reviving Boston's historic markets with food stalls, cafes, restaurants, and pushcarts.
Thompson separated from the Collaborative in 1966, and started his own firm, Benjamin Thompson and Associates (BTA). His five-story, all-glass showcase for Design Research opened in Cambridge, Massachusetts in 1970. (As of 2005 it houses Crate and Barrel.)
He is probably best known for a series of collaborations with the developer James W. Rouse, including the Faneuil Hall Marketplace (1976), Harborplace (1980), South Street Seaport (1985), Bayside Marketplace in Miami (1987), and Jacksonville Landing in Jacksonville, Florida (1987).
Thompson was married to Mary Okes, with whom he had 5 children: Deborah, Anthony, Marina, Nicholas, and Benjamin.
His second marriage was to the urban planner Jane McCullough Thompson, with whom he collaborated on many of his major projects. He received honorary doctorates from Colby College, the University of Massachusetts, and Minneapolis College of Art and Design. In 1987 BTA received the AIA Firm Award and in 1992 Thompson received the highest honor in American architecture, the Gold Medal of the American Institute of Architects.