It was named after Thomas Becket whose cult pilgrimage to Canterbury began at London Bridge.

The church was renamed St Thomas the Apostle following the abolition of the Becket cult in 1538 during the Reformation.

The present church was built by the Hospital Governors to designs by Thomas Cartwright in 1703.

The building was undermined by the Jubilee Line Extension workings and was 'at risk' but repairs were effected from 2010 it became the HQ of the Cathedral Group property development company.

The scientific facility was uncovered in 1957 by Raymond Russell, and is situated in the garret (roof section) of the church.