Congregationalism is a form of church government adopted by those Protestant Christians known as Congregationalists. Congregational churches assert the autonomy of the local congregation insofar as each congregation manages its own affairs. Its members believe in a covenant of loyalty and mutual edification, emphasizing the importance of discerning God's will whilst ‘gathered’ together in Church Meeting. Their historical roots are in Elizabethan Separatism with its insistence that the "gathered church" consists of those who commit themselves to Christ and each other.

The first Congregationalists established themselves in London, England, and were called the Brownists after Robert Browne, who defined the congregational principle in 1580. They arose from the Nonconformist religious movement during the Puritan reformation of the Church of England. Early congregationalists were called separatists or independents.

The model of Congregational churches in North America was established by the settlers at Plymouth, Mass. (1620), a Christian fellowship, and the Puritans at Massachusetts Bay (1630). When the Pilgrims landed they endured months of hardship. In their day, the challenges they faced are akin to going to Mars. The journey across the Atlantic Ocean was treacherous at best, especially for a bunch of non-sailors with families transporting all their earthly belongings. And, upon arrival, the real problems began. Nevertheless, their commitment to personal and religious freedom enabled them to overcome all obstacles. Many were regarded as "separatists," simply Congregationalists who wanted the freedom to worship as they pleased.

The settlers rejected the episcopacy form of Church rule because they disagreed with the concept that bishops should rule their spiritual lives. Believing the Holy Spirit worked in them individually as well as any Church official, they felt able to decide spiritual matters for themselves. They then took the very radical step of doing so. Now, the congregation would decide matters of spiritual import. This had seldom ever been done before and they found themselves willing outcasts.

The Puritans, settling north of Plymouth in Massachusetts Bay, sought to establish a "theocracy" where, instead of man-made rules to guide them, biblical standards would guide them. While not nearly as harsh or rigid as some historians would later suggest, Puritans were strict and in some cases as intolerant as the Church and society they had left behind. As in England, some followers were banished, some were punished physically, and still others were put to death for reasons that seem repulsive today.

The model of Congregational churches was carried by migrating settlers from New England into New York and the Old Northwest: Ohio, Indiana, Michigan and Illinois. With their insistence on the independence of local bodies, they became important in many reform movements, including those for abolition of slavery, and women's suffrage.

From the early 20th century and beyond several congregations and churches merged resulting in what is known today as the United Church of Christ. Other churches and congregations merged into smaller denominations that still practice Congregational rule.

While Baptists and others practice congregational-type rule, those who practice Congregationalism include the Congregational Christian Churches, Conservative Congregational Christian Conference and the United Church of Christ.