In 1826 St. John's was founded as a mission church of the diocese of Quebec by the newly ordained deacon Samuel Armour who began services in the local school house.

In 1834, the small congregation was granted a block of land strategically situated on a hill just west of the Otonabee River overlooking what became downtown Peterborough. Built from locally quarried stone, the church as the first stone Anglican church of Gothic design in British North America. The cornerstone for a new church was laid in 1835 on land especially granted to the congregation and regular services have been held in the Church since February 1837.

Over the past 170 years there have been a number of renovation and restoration projects designed to serve a dedicated, vibrant, and growing parish community. In 1882, the first major restoration added the sacristy and chancel wings, and the tower top was changed from pinnacles to battlements. The tower doors became the main entrance and in 1911, the tower was fitted with the People's Chime, which was then and still is, the largest set of bells between Toronto and Ottawa. In 1957, the church members completed an ambitious and imaginative building project connecting the church and the Guild Hall. In 2007, St. John's embarked on a campaign to make improvements and renovations to allow forward movement in the ministry of the church. In January 2010, the church celebrated the completion of a number of projects designed to welcome our community, conserve our environment, and enhance our worship.

St. John's is rooted in the Anglican tradition, a tradition that traces its origins to the Reformation in the sixteenth century. Since the Reformation heritage, Anglicans have sought to restore a high valuation of the worship practices of the earliest Church. Its celebrations of worship have a rich deposit of customs that can be traced through the centuries to the life of the earliest Christians. Central to Anglican worship is the twin emphasis of the celebration of the sacraments and the hearing of God's Word. Also, from the nineteenth century onward, Anglicans have played a prominent role in recognising and addressing the social dilemmas that plague the world.

Historically, Anglicans have understood themselves as being a fellowship within the "One, Holy, and Apostolic faith" as set out in the Book of Common Prayer. While various national communions have written revised prayer books in the twentieth century, Anglicans remain, generally, those who place a high value on an ordered form of worship and belief as contained in a standard guide. In addition, Anglicans have been organised into national Communions in fellowship with each other through a council of bishops joined together in mutual love and respect.

In these beautiful surroundings, the community that is St. John's has been worshipping and ministering to each other and to the people of Peterborough and area for almost 200 years.