Born in England, a younger brother of John Stoughton, he emigrated to New England in 1632. He settled at Dorchester, of which he was admitted a freeman on 5 November 1633. He was chosen representative for Dorchester in the assemblies of 1634 and 1635.
When the colony was disturbed by the Antinomian Controversy, Stoughton wrote a book which attacked the constitution of the colony and offended the general court. The author somewhat strangely petitioned that the book might be ‘forthwith burnt, as being weak and offensive.’ In spite of Stoughton's subsequent submission, he was declared incapable of holding office for three years. This sentence, however, was remitted in 1636, and Stoughton was chosen assistant in 1637.
He was entrusted with the command of the Massachusetts force against the Pequot Indians, where he took brutal measures. Stoughton was annually chosen as assistant till 1643, and in 1639 he, together with John Endecott acted as a commissioner on behalf of Massachusetts to settle a boundary dispute with Plymouth Colony.
Stoughton visited England towards the end of 1643 or the beginning of 1644, returned to America, and crossed again towards the end of 1644. He was then appointed a lieutenant-colonel in the parliamentary army, and soon afterwards died at Lincoln. His children included William Stoughton, best known as the chief magistrate of the Salem witch trials.
- Thompson, Roger. "Stoughton, Israel". Oxford Dictionary of National Biography (online ed.). Oxford University Press. doi:10.1093/ref:odnb/26605. (Subscription or UK public library membership required.). The first edition of this text is available as an article on Wikisource: "Stoughton, Israel". Dictionary of National Biography. London: Smith, Elder & Co. 1885–1900.