Whitehouse was born in New York City, New York, the son of Mary Celine (née Rand) and career diplomat Charles Sheldon Whitehouse, and grandson of diplomat Sheldon Whitehouse (1883–1965). Among his great-great-grandfathers were Episcopalian bishop Henry John Whitehouse and railroad magnate Charles Crocker, who was among the founders of Central Pacific Railroad. Whitehouse graduated from St. Paul's School in Concord, New Hampshire, and from Yale University in 1978. He received his Juris Doctor (J.D.) from the University of Virginia School of Law in 1982.