The land eventually called Haverhill was first settled by Puritans in 1640. In 1641 Rev. John Ward, from Haverhill England, came to the young settlement and became the first minister; the town was incorporated in1641 and named Haverhill after Ward’s birthplace. The town lands were formally purchased from the Pentuckets in 1642. Rev. Ward was officially installed as the pastor of the First Parish in 1645 and the first meeting house was constructed in 1648. Rev. Ward served as the minister until his death in 1693. He was followed by Rev. Benjamin Rolfe and was installed in 1694. Construction on the second meeting house began in 1697 and was completed in 1699.

The town of Haverhill was separated into multiple parishes during the early eighteenth-century. In 1728 the town was divided into two parishes with the formation of the North Parish. The North Parish was transferred to Plaistow, New Hampshire in 1741 and the Rockingham Congregational Church was formed. In 1734 the town was divided yet again with the formation of the West Parish and the East Parish was formed in 1743. In 1748 a bell, imported from London, was installed in the First Parish church. The third meeting house was constructed 1766.

Rev. Dudley Phelps, a strict orthodox Congregationalist, was installed as the pastor of the First Parish in 1828. His strict orthodoxy became a point of contention and the parish dissolved its relation with Rev. Phelps in 1832. The First Parish, which kept the third meeting house, became a Unitarian church after the split. In 1833 the Independent Congregational Church and Society was formed with Rev. Joseph Whittelsey as its first minister. In 1840 the name was changed to Centre Congregational Church and Society. The new church originally worshipped at the Summer Street Church and Academy Hall until 1834 when a new church building was constructed. The church had a small separation in 1839 when seventeen members withdrew to form the Union Evangelical Church of Haverhill. That church was later renamed to the Winter Street Church. The winter street church was dissolved in 1860. By 1859 the Centre Congregational Church had grown significantly and it was decided that a portion of the parish would leave to form a new church in the north of Haverhill. In 1859 100 former members of the Centre Church formed the North Congregational Church. In 1891 some members of both the North and Centre Congregational Churches joined together to form the Union Congregational Church. The Union Congregational Church dissolved in 1932.

The first building of the North Congregational Church was completed in 1860. In the early twentieth-century, the building was renovated with Tiffany memorial windows. In 1929 the North Parish Community Church was formed after the dissolution of the Rockingham Congregational Church in Plaistow, New Hampshire. In 1940 the Centre Congregational Church and North Congregational Church merged to form the First Congregational Church in Haverhill which occupied the North Church building. In 1963 the North Parish Community Church merged into the First Congregational Church; at the same time the First Congregational Church joined the United Church of Christ. In 2010 the 1860 church building was sold and the First Congregational Church was formally dissolved.