William Stoughton was born on September 30, 1631 in England. His parents, Israel and Elizabeth Stoughton, owned a great deal of land in the Massachusetts Bay area. From an early age, Stoughton was interested in the ministry. At age nineteen, he earned a degree in theology from Harvard College, then returned to England where he received an M.A. from Oxford in April 1652. Stoughton continued his studies at Oxford until he lost his fellowship in 1660.
Two years later Stoughton left England for the colonies, finding a job as a preacher in a Dorchester, Massachusetts church. Stoughton was generally praised for his preaching ability and offered the job of church pastor.
Following the revocation of the Massachusetts Charter and the reassertion of English control over the colony, Stoughton entered political life. He served as a Deputy President of the colony's temporary government from 1674 to 1676 and from 1680 to 1686. This position put him in charge of the colonial courts of justice. From 1676 to 1679 he also acted as an agent for Massachusetts at the Court of Charles II in England.
Although he lacked any legal education, Stoughton was appointed Chief Justice of Massachusetts, a position he continued to hold until shortly before his death.
Following the outbreak of witchcraft accusations in Salem, Phips appointed Stoughton chief justice of the newly formed Court of Oyer and Terminer. Stoughton, possibly because of both his past theological training and lack of legal training , allowed many deviations from normal courtroom procedure during the witchcraft trials. In addition to admitting spectral evidence, the court allowed private conversations between accusers and judges, permitted spectators to interrupt the procedures with personal remarks, forbid defense counsel for the accused, and placed judges in the role of prosecutors and interrogators of witnesses. Although he acted as chief justice in the Court of Oyer and Terminer during the Salem witches trials, Stoughton suffered little political damage. In 1694, he became acting governor when Phips returned to London to defend his administration against claims of corruption. Stoughton died on July 7, 1701.