Educated at Trinity College, Cambridge, Cotton became vicar of the parish church of St. Botolph's in Boston, Lincolnshire, in 1612 and remained in that post for 21 years. During this time he gradually became more Puritan in his outlook, and he ceased to observe certain Anglican religious rituals in his performance of his duties. In 1632 legal action was taken against him for his Nonconformism, and in July 1633 he emigrated to the Massachusetts Bay Colony, where he became “teacher” of the First Church of Boston, remaining so until his death. His popularity in the colony was unbounded, and his influence in both civil and ecclesiastical affairs was probably greater than that of any other minister in theocratic New England.

Cotton wrote several works that constitute an invaluable exposition of New England Congregationalism, including The Way of the Churches of Christ in New England (1645) and The Way of Congregational Churches Cleared (1648). The catechism he wrote, Milk for Babes, Drawn out of the Breasts of Both Testaments (1646), was widely used for many years in New England for the religious instruction of children.