The church is thought to stand on the site of a church built for the local Christian community in Roman times. It was rebuilt on its original site, which is just off the main street in Canterbury. It was rebuilt by St Augustine and his monks in Anglo-Saxon days. Evidence of its early origins can be seen in the tower, which incorporates Roman tiles, and Anglo-Saxon quoins or cornerstones. The tower in its present form dates from c.1100 and houses four ancient church bells, cast between c. 1325 and c. 1599.
In 1448, King Henry VI established the Mayoralty of Canterbury, from which date all the names of the Mayoralty are recorded. The mayor-making service was held in St Peter's church where, from 1660, the rest for the mayoral mace and sword can be seen. Many of the City's past mayors are buried inside the church as well as in the churchyard. Parish registers begin on 9 September 1590. By the middle of the 1600s, the parish of St Peter's was home to many Huguenot and Walloon refugees. They had fled their countries to escape religious persecution. Inside the church on the north wall is a brass commemorating these settlers, who were buried in the churchyard.
In 1681, St Peter's was united with the adjoining parish of Holy Cross. This connection only ended in 1959. Until 1910, there was a close association with St Augustine’s Missionary College and services were undertaken by Warden Maclear, the Fellows and students. Unfortunately, in 1926, services were suspended and the church was gradually denuded of most of its furnishings, including the organ. In 1953, Sunday services were reintroduced. Six years later, with the reorganisation of the parishes and a new Rector, St Peter's was once again restored to its full life. In 1974 the parish of St Peter and St Alphege with St Margaret, and St Mildred with St Mary de Castro was formed. In 2017, the Benefice of St Dunstan, St Mildred and St Peter was created.
St Peter are open during services on Sunday and every Wednesday at 12.30pm.