Recorded since the 12th century, the church was destroyed in the Great Fire of London of 1666, then rebuilt by the office of Sir Christopher Wren.

In part it reads: St Martin, Ludgate, also has the bread shelves from St. Mary Magdalen Old Fish Street.

On Easter Day 1653, John Evelyn recorded in his Diary that he and his family received Holy Communion at St. Mary Magdalen's.

[3] Between 1824 and 1842, the rector of St. Mary Magdalen's was the Reverend Richard Harris Barham, author of The Ingoldsby Legends.

On the morning of Thursday, 2 December 1886, a fire broke out in a warehouse in what by this time was called Knightrider Street and spread to the church's roof, causing substantial damage.

The opportunity was taken to pull down St. Mary Magdalen's and combine the parish with that of St Martin, Ludgate, which received some of the furnishings from the demolished church.

The site previously occupied by St. Mary Magdalen's was built over after the Second World War, and is now covered by Old Change Square.