William Howard Stein (June 25, 1911–February 2, 1980) was an American biochemist who was born and died in New York City. Stein won a Nobel Prize in Chemistry in 1972 with Christian Boehmer Anfinsen and Stanford Moore, for their work on ribonuclease and for their contribution to the understanding of the connection between chemical structure and catalytic activity of the ribonuclease molecule.

In 1958 he and Stanford Moore developed the first automated amino acid analyzer, which facilitated the determination of protein sequences.