Some Congregationalists claim that Congregationalism began with Jesus himself, when he gathered ordinary people around him during his earthly ministry. These little groups of people, it may perhaps be said, were the first Congregational churches. These people loved their Lord, and they desired His presence with them. When they urged Him to stay, He replied that He must go to other cities. They found, however, that when His physical presence was withdrawn, they were still conscious that He was there in might and power when they gathered in His name. Some would say that this is to ante-date the beginning of the Christian Church.Certainly after the death and resurrection of Christ, wherever the gospel was preached and those who had been saved by its power were gathered together, they found that Christ's words were true, "Where two or three are gathered together in my name, there am I in the midst of them".

People came to believe in Jesus as Lord, and naturally joined with other believers for worship, mutual edification and Christian service. These little groups listened to the counsel and warning of the apostles, but they arranged their own business, setting apart their members for special tasks - deacons to look after the material needs of the poor, bishops or presbyters (sometimes called elders) for the work of the ministry. The one thing that made men and women members of the Church was faith in Christ, and all members were "called to be saints" and thus the church was a communion of saints.

The early churches were acutely conscious of two things:-

1.That Christ was their Head, their Leader and Guide, and that they had direct access to Him. With Him they needed no control from without by either civil or ecclesiastical power: they were independent, and competent with His guidance to settle all the details of their own worship, administration and government.

2.At the same time they had an intimate sense of union with all other Christian communities. They all belonged to the one Church; they were all branches of the one "living vine"; they had all the same task of winning the world for their Lord, and they desired to co-operate together in it to strengthen one another and in every way realise and manifest their unity and make their witness for their Lord efficient and powerful.

Thus some Congregationalists have argued that the Apostolic churches were Congregational or Independent, their government not being in the hands of bishops or presbyters so the early churches were neither Episcopal or Presbyterian. As time went by the simplicity of the early church disappeared, and eventually civil authorities began to regulate the life of the church after the church was recognised by the Roman Empire. In the Middle Ages the church was controlled by Prince Bishops who were often interested in worldly power rather than the cause of Christ. This process continued until the Reformation, the Church pursuing its course through wealth, unreality, and decay until the beginning of the sixteenth century. But Congregationalism did not die; it only vanished underground, for its principle is inevitable. Wherever men and women are won for Christ they desire to come together for worship, mutual help and united service, and every such group, once it begins to function in its principle is a Congregational church, though its members may know nothing of polity, and their theory of church government may never be made explicit. It is probable that at no time since the death of Christ has the world been entirely without the Congregational witness.

In England, modern Congregationalism began with the followers of John Wyclif. Men and women called the Lollards, met together in woods and fields to hear the Bible read in their own language. As the English Reformation progressed in the sixteenth century, many men and women called for a more reformed church. During the reign of Elizabeth I, many who had been influenced by the continental Reformation believed that the Church of England still contained the "remnants of Popery". In 1567, some small groups of Christians were meeting together independently of the Church of England. The best known of these congregations was the one which met in the Plumber's Hall, London. It seems to have contained as many as a hundred people, of whom number were in time imprisoned for holding illegal religious worship. These men and women had separated themselves from what they believed was only a partially reformed Church of England. They were known as Separatists. In 1593, John Penry, Henry Barrow, and John Greenwood were hanged for their dissent from the Church of England. There were other martyrs around the country, and many Separatists died in prison. Robert Browne, meanwhile wrote his famous Treatise of Reformation without Tarrying for Anie. In this book Browne expounded the principles of Congregationalism. In 1620, a groups of Separatists who had fled to Holland with their minister, John Robinson, sailed to New England in the Mayflower and are known as the Pilgrim Fathers. In New England they established a Congregational church. In the 1630's Congregationalism in New England grew with the emigration of Puritans from this country.

Whilst the Separatists worshipped outside the Church of England, many people who longed for further reformation of the English church continued to work within this church. These people were called Puritans because they wished to purify the church. During the English Civil War, a conference at Westminster produced the Westminster Confession of Faith. This statement of faith is still seen today as a great declaration of the Reformed Faith. After the Civil War, Congregationalism as Cromwell himself was a Congregationalist. In 1658, just after Cromwell's death, two hundred representatives from 120 Congregational churches met at the Savoy Palace and produced the Savoy Declaration of Faith and Order. This statement is the most admirable statement of the ecclesiastical principles of English Congregationalism. With the restoration of the monarchy, persecution of Congregationalists and other Dissenters became very severe. In 1662, almost two thousand Puritan ministers were ejected from the Church of England by the Act of Uniformity. Many ministers continued to preach to their followers and many Congregational churches trace their formation to this date. With the Act of Uniformity, English Nonconformity was permanently established. Persecution continued until 1689, when the Toleration Act was passed. Dissenters were now able to build Meeting Houses and register these buildings as places of worship.