The original Church of St. Magnus the Martyr was built on this site in 1176. It was destroyed by the Great Fire of London in 1666, and was then rebuilt by Sir Christopher Wren in 1676. The tower was added in 1704, taking the building to its current height.
St. Magnus the Martyr used to stand at the northern end of old London Bridge, and when the bridge was widened a roadway was built through the base of the church's tower. When the bridge was demolished in the 1880s, the replacement was built further upstream.
Some stones from the old London Bridge remain in the churchyard, along with the remains of a Roman wharf.