In the summer of 1833, the Rev. John Morrice Roger, a young Presbyterian minister, fresh from college in Scotland, arrived in the community to serve with the Glasgow Missionary Society. This 26 year old son of a minister soon showed evidence of his ability as a born leader, and the considerable number of Presbyterians already here quickly gathered about in him in small groups - not only in Peterborough itself, but also at various outlying points.
In 1834, Rev. Roger formed all these people into a congregation and this new body was recognised as a properly constituted court of the church by the Presbytery of Kingston (in connection with the Church of Scotland) and was known as the First Presbyterian Church of Peterborough. However, in the wake of the Disruption of 1843, Rev. Rogers was one of a group of ministers who favoured separation from the Church of Scotland. This group constituted themselves into a new synod under the name of the Presbyterian Church of Canada.
For fourteen years, the congregation still worshipped in the old stone kirk on the hill (the site of the present St. Andrew’s United Church in Peterborough) until a formal demand was served on the minister and session for possession of the church property by the Synod of the Presbyterian body in Canada that still adhered to the Church of Scotland. Rev. Rogers had no alternative but to find another site, so on land donated at the present site of St. Paul's, the erection of a new church began. The church was opened in 1859 at a cost of $20,000.
In 1883, the sides of the church building were extended outwards to form the East and West wings giving the sanctuary a seating capacity of over 1000 which, along with the addition on the North end of the sunday school auditorium and classrooms, cost the congregation a further $24,960.00.
In May, 1885, the formal opening of the reconstructed St. Paul's took place. In addition to the rededication ceremonies, a new pipe organ at a cost of $3000 was dedicated to the worship of God in connection with service of praise. This organ was a tribute to the skill of the organ builders from St. Catherines.
In 1959, at a cost of $120,000, a new Christian Education Centre was added to the east side of the church on the site of the old stables.
The General Assembly of the Presbyterian Church in Canada has been held in St. Paul's twice, 1933 and 1984. In 1984, Dr. Alex Calder, minister of St. Paul's at the time, became Moderator.
St. Paul's has had 12 ministers in its history - the present minister is the Rev. Jonathan Baird who was ordained and inducted in May 2013.