The patronage of the church belonged to the canons of St Paul's and it is mentioned in the register of the Dean and Chapter as early as 1181.

[1] John Stow implies that was rebuilt some time in the late fourteenth century, describing John Barnes, Lord Mayor in 1371 as "a great builder of S. Thomas Apostles parish church as appeareth by his armes there both in stone and glasse".

[1] The parish was staunchly Royalist[3] in the years leading up to the Civil War[4] In 1642, the rector, named Cooper, was sequestered and imprisoned in Leeds Castle owing to his loyalty to the king.

Following the fire, a Rebuilding Act was passed and a committee set up under Sir Christopher Wren to decide which buildings would be rebuilt.

[1] The site of the church is marked by a plaque in Great St Thomas Apostle Street near Mansion House tube station.