The first St Thomas was founded in 1767 and completed by 1773 but not consecrated as a Chapel of Ease under the Mother Church of Eccles until the 6th July 1776. One half of all fees gathered were submitted to the Vicar of Eccles. The original site was on Brindleheath Road a few hundred yards to the North West of its present position.

By 1829 the church was too small for the rapidly expanding population and King George IV granted a triangular portion of "the wastes of Penhilton" called Pendleton Green, to erect a new church where it still stands today somewhat isolated by the road and underpass system overlooking the new Salford Precinct. It was consecrated in October 1831 by the Bishop of Chester; the money for the building of the Church came from the "Million Fund". (An act of Parliament in 1818 granted £1 million to finance the building of new churches throughout England. Such churches were known as "Waterloo Churches", the nation's thanksgiving to God for the victory over Napoleon at Waterloo).

The old chapel of ease was abandoned leaving it in a state of dilapidation until the cholera epidemic of 1849, when it was used as an isolation hospital. The site was reused when the first church of St Anne was built there, building work being started in 1863. It in turn was abandoned in 1914 when the new church of St Anne was built on Sharp Street near the bottom of Brindleheath Road as part of the cycle of matching the growing population; a cycle that was reversed by the slum clearances of the 1950's and 60's when much of the population of Pendleton was rehoused in new estates in Kersal, Little Hulton and elsewhere.