John Cotton (4 December 1585 – 23 December 1652) was a clergyman in England and the American colonies, and by most accounts was the preeminent minister and theologian of the Massachusetts Bay Colony. Following five years of study at Trinity College, Cambridge, and another nine years at Emmanuel College, Cambridge, he had already built a reputation as a scholar and outstanding preacher when he accepted the position of minister at Saint Botolph's Church in Boston, Lincolnshire in 1612. As a Puritan he wanted to do away with the ceremony and vestments associated with the established Anglican Church, and preach in a simpler, more consensual manner. Though he felt the English church needed significant reforms, he nevertheless was adamant about not separating from it; his preference was to change it from within. While many ministers were removed from their pulpits for their puritan practices, Cotton thrived at St. Botolph's for nearly 20 years because of supportive aldermen, lenient bishops, and his very conciliatory and gentle demeanor. By 1632, however, the Anglican church had greatly increased its pressure on the non-conforming clergy, and Cotton was forced to go into hiding. The following year he and his wife boarded a ship for New England.

Cotton was highly sought as a minister in Massachusetts and was quickly installed as the second pastor of the Boston church, sharing the ministry with John Wilson. He generated more religious conversions in his first six months than had been made the previous year. While early in his Boston tenure Cotton became only peripherally involved in the banishment of Roger Williams, Williams blamed much of his troubles on Cotton. Soon thereafter Cotton became embroiled in the colony's Antinomian Controversy, when several adherents of his "free grace" theology, most notably Anne Hutchinson, began criticizing other ministers in the colony. While he tended to support his adherents through much of the controversy, it was not until near its conclusion that he came to realize that many of his followers held theological positions that were well outside the mainstream of Puritan orthodoxy, which he did not condone.

Following the controversy, Cotton was able to mend fences with his fellow ministers, and he continued to preach in the Boston church until his death. A great part of his effort during his late career was devoted to the governance of the New England churches, and he was the one who gave the name Congregationalism to this form of church polity. In the early 1640s as the Puritans in England gained power on the eve of the English Civil War, a new form of polity for the Anglican Church was being decided, and Cotton wrote numerous letters and books in support of the "New England Way". Ultimately, Presbyterianism was decided as the form of governance during the Westminster Assembly in 1643, though Cotton continued to engage in a polemic contest with several prominent Presbyterians on this issue. As Cotton became more conservative with age, he not only battled the separatist attitude of Roger Williams, but also agreed with the severe punishment, including death, of those whom he deemed were heretics such as Samuel Gorton. A scholar, avid letter writer, and author of many books, Cotton was considered the "prime mover" among New England's ministers. He died in December 1652 at the age of 67, following a month-long illness. His grandson, Cotton Mather, also became a prominent New England minister and historian.