It is believed a church has existed on this site since Saxon times.
Saxon churches were rebuilt by Norman craftsmen after the Conquest and it is recorded that the third church of St Mary Maldon was completed in 1130.
The tower was added in 1300 but collapsed in 1605 also damaging the church. Due to the importance of this landmark to mariners a petition was sent to King Charles I. It was sucessful and work to rebuild the tower in red brick and repair the damage to the church was completed in 1636
A beacon was was lit at the top of the tower to guide ships returning home to the Hythe. The addition of the white shingled spire in 1740 further increased the height and visibility to mariners.
Further restoration works were completed in 1886 which included work to a new chancel and north isle. A new roof was added with massive Baltic timbers carrying thousands of tiles from the old roof.
In more recent years the church was enhanced by the addition of a new window in the south wall commemorating the battle of Maldon in 991. In the latter part of 2015, a new pipe organ was installed on the west wall.
The church is normally open to view during the day.