Stoughton graduated from
Harvard College in 1650 with a degree in theology. He intended to become a
religious minister and continued his studies in
New College, Oxford, graduating with an M.A. in Theology in
1652. The Kingdom of England had by then been replaced by the
Commonwealth of England.
Stoughton received a
Master's degree in June 1653. The same year the Commonwealth was replaced by
The Protectorate of
Lord Protector Oliver Cromwell.
Stoughton served as a
curate in
Sussex during the
English Restoration of 1660. He was a
Puritan at a time when this denomination was strongly connected to the recently deceased Cromwell. They fell out of favor with the Restoration of
Charles II of England to the throne. Stoughton would not hold his position for long.
Having lost his position as a curate and having little chance to gain another, Stoughton returned to
Massachusetts in 1662. He served in various positions in the colonial government, including as
Joseph Dudley's deputy in 1686. By the early 1690s he was colonial chief magistrate, the first Chief Justice of the
Massachusetts Supreme Judicial Court. In 1692 he acted as judge and prosecutor during the
Salem Witch Trials, notoriously allowing
spectral evidence and denying the accused
defense counsel.
Stoughton was acting
Governor of Massachusetts from 1694 to 1699, while still serving as Chief Justice, and again from 1700 to 1701. He was an adroit politician who managed the factions of the Colony's politics using the power of his governorship and judgeship and appointments to both his council and to lower courts.
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