The church was not the only building in need of repair, and a fundraising campaign, led by the President of the hospital, Sir Robert Clayton, was already underway with the aim of completely rebuilding the hospital. By the early 18th-century, the hospital was transformed into an elegant classical edifice. St Thomas's Church was rebuilt between 1698 and 1701, with interior decoration and fittings following over the next few years.
The new building was built in the style of Christopher Wren. At this time Wren was a governor of the hospital and he or one of his design team may have been involved with the design. However, recent opinion is that it was substantially designed by the Master Mason, Thomas Cartwright. Cartwright worked as Master Mason on three Wren churches across the river in the City, including St Mary Le-Bow. The rebuilding cost £3718, including compensation to the owners of two small houses to the east of the old church which were also pulled down. This suggests that the previous church had occupied the west end of the present building. It was also built on a slightly different alignment. The church is all that survives from this rebuilding campaign, and is therefore the oldest part of the hospital.
The Church was renamed in the Reformation and lost its designation to Thomas Beckett in exchange for St Thomas the Apostle. Clearly the authorities were keen to end any association with a pro-Catholic Martyr but were unsure that the local population would take to a radical renaming. The change to St Thomas the Apostle was therefore convenient.
In the 19th-century the church was made redundant and became the Chapter House of Southwark Cathedral. In the 1980s the church was taken over by the Chapter Group who are Lloyd's insurance brokers. The Old Operating Theatre Museum remains in the roof space of the church.