The foundations of St Thomas' Church were laid in 1866 and the church was formally opened on the 27th May 1868.

Prior to 1866 there had been a small Catholic community in the town of Gainsborough and Mass had been celebrated in various rented rooms in the town.

In 1866 Thomas Arthur Young of Kingerby funded the building of St Thomas' Church and the adjoining presbytery which were completed at a cost of £1,200 exclusive of land.

Thomas Arthur Young commissioned the architect Matthew Ellison Hadfield (1812-1885) to build the church in Gainsborough. Hadfield was an early follower of the Gothic Revival movement led by A W N Pugin.

The exterior of St Thomas' is very plain. Pre-World War One photographs of the church show an extremely ornate interior of which virtually nothing is left today.

The Catholic Community in the Gainsborough area since 1823 has been served by at least 38 priests, the church has had three new altars, at least five major refurbishments, two fonts, two organs, two sets of Stations of the Cross depictions and several statues, most of which are no longer in place, and three tabernacles.

Some of the major refurbishments were due to having a damp problem which affected the original wooden altar. The church also took advantage of modernisation at various stages, changing from gas lighting to electricity and installing new heating systems.

The most recent refurbishment in 2008 has taken the church back to its Pugin style roots with the Sanctuary being decorated with hand blocked Pugin style wallpaper and the overall effect is more reminiscent of the original church.