It is possible that the original church of St Mary’s was Saxon in origin, although there is little concrete evidence to this effect. What is certain is that the church was built on the site of a Roman structure. The tower and western part of the nave date from the 11th century. This Norman church was built between 1066, when Saxon Dover was destroyed by the Norman invaders, and 1086, when the Domesday Book lists three churches in Dover. Although not named it has been assumed that the three churches were St Mary’s, St James’and St Peter’s.

The church is mentioned in a list of possessions of Dover Priory in 1180. In 1230 St Mary’s passed into the control of the Maison Dieu, the Master providing priests for the church until the Dissolution in 1537, when the church was closed. The townspeople petitioned Henry VIII to let them have St Mary’s as a parish church, and this was granted in 1544.

In 1581 the Mayor and Corporation moved their official place of worship from St Peter’s Church, which had fallen into disrepair, to St Mary’s. Since then the church has been associated with civic bodies, the Mayor and Corporation, the Cinque Ports Pilots of Trinity House, and the Dover Harbour Board, all have official seats in the church.

The Mayors of Dover and Members of Parliament for Dover were elected in the church from 1581 until 1826. A barrier was placed down the centre of the building to keep the rival factions apart, and often there was bloodshed and the church desecrated and made unfit for public worship.

St Mary’s present form dates from the controversial restoration carried out in 1843 by the then Vicar, Canon John Puckle. It was less restoration and more complete rebuilding. The church was enlarged, the south aisle extended to balance the north aisle, and the roof raised and clerestory windows added. During the rebuilding, original Norman piers and arches were taken down, the stones numbered and then re-erected in their new position. Only the tower escaped relatively untouched. So the church as it is seen today is mainly a Victorian construction.

St Mary’s is still very much the town’s parish church. Many of the stained glass windows, put in to replace those destroyed in World War 2, commemorate the various historic associations between the church and town.