In August 1662, Thomas Lowry of Market Harborough and Matthew Clarke of Narborough were among several thousand ministers ejected from the Church of England for refusal to agree to the forms of worship and organisation of the national church. People of a Congregational persuasion believed that the church should be made up only of believers rather than automatically including everyone in a parish. They also believed that there should be no other authority in the church than Jesus Christ and hence had no truck with bishops or hierarchy of any kind.

In Harborough and surrounding villages, groups of Congregationalists began to meet in homes, cowsheds, woods and anywhere they could avoid those trying to enforce the law which banned the assembly of such groups. Matthew Clarke was one of a number of ministers who led worship and provided support. For doing this, Matthew spent several periods in Leicester Jail. However, in 1689 the Act of Toleration allowed him to be licensed to preach and in 1694 he and his fellow church members built a Meeting House in Bowden Lane at the bottom of Burnmill Road. Worship continued in this building until 1844, when the old Meeting House was pulled down and the present chapel built.

Though they were allowed to worship openly after 1689, Congregationalists were still barred from the universities and from public office at local and national level. As a result, they set up their own educational academies, one of which was established in Harborough in 1749 by Rev Philip Doddridge, though later the same year he moved, with his academy, to Northampton. Dr Stephen Addington, minister 1753 to 1781, also established an academy, in his case in the Mile End, London. These academies taught a wide range of arts and sciences. Soon after this the Sunday School began in the town teaching children to read, as well as grounding them in the Bible and Christian faith. At its height in the 1880s, the Sunday School had around 500 pupils and the Jubilee Hall was built to house them.

Denied access to public office, many Congregationalists put their energy and enterprise into business and the professions.  Through the last few centuries they controlled much of the commerce in the town in businesses as diverse as wool merchant, hat maker, tinsmith, blacksmith, cabinet maker, saddler, butcher, baker, grocer, postmaster, agents for the railways and insurance companies, as well as solicitors, architects and bankers. At the end of the eighteenth century about a quarter of the households in Harborough were Congregational and until well into the twentieth century a good proportion of the businesses which lined the High Street were in their hands.

In the 19^th Century the Congregational Chapel sent missionaries to what is now Zambia, Madagascar, India, Samoa and Kiribati.

In the middle of that century many Harborough Congregationalists became embroiled in the Church Rates Controversy. Local government was still under the control of the Church of England parish priest and his church wardens. Everyone had to pay taxes to them which went in part to pay the running costs of the parish church. Those of other denominations objected and withheld their rates. As a result several Congregationalists had property seized in lieu and some were arraigned before the Kings’ Bench. In the end, their stand contributed to the changing of local government law, with the introduction of Urban and Rural District Councils. Once these were established, Congregationalists, by now allowed to enter government, played major roles into the middle of the 20^th Century, including H H Pickering who was chairman of Harborough UDC 1923-24 and 1928-45.

In 1972, when many Congregational Churches in England and Wales joined with the Presbyterians in the United Reformed Church, Market Harborough decided to remain an independent congregation. It joined with churches who had made a similar decision to form the Congregational Federation. Strong links with the Baptist and Methodist Churches in the town continued throughout the twentieth century and this cooperation was widened as the 21^st Century approached to include other churches in the town in Churches Together in Harborough, through which it has become involved in the Bower House Christian Counselling Service, the Street Pastors, The Cube youth project and much more. Most recently it has been instrumental in establishing the Jubilee Foodbank. The buildings to the rear of the church, including the Jubilee Hall were extensively refurbished for church and community use in 2000.

In July 2015 Rev Stephen Haward MA was called to the ministry of this church.