This church seems to be in the very centre of the city and is quite difficult to view overall owing to the number of buildings around it. It is in fact sited in one of the first areas to be settled when the city grew up to the north of the new cathedral in the first half of the 13th century. It is first mentioned in 1238 and the parish of St. Thomas existed by 1246. A cruciform church, built during the first half of the 13th century is thought to form the core of the present building. In the second half of the 13th century a chapel was built against the southern side of the chancel, possibly this was St. Stephen's chapel, and in the late 14th century the Godmanstone chantry was built on the northern side. The bell tower was being built between 1400 and 1404 and at that time was separate from the church.
In 1447 the roof of the chancel collapsed and was rebuilt, largely by gifts from wealthy parishioners such as William and Henry Swayne, John Hall and the Godmanstone family. In 1448 William Swayne founded two chantries, one for his family and one for the tailor's guild. Much other rebuilding seems to date from this period. The three storied vestry built to the north of the north chancel aisle in 1462-7 may have provided accommodation for the chantry chaplain. The whole body of the church was remodelled in the late 15th century providing a lofty clerestoried nave with a north and south aisle, and the northern side of the bell tower became part of the southern wall of the south aisle as it was incorporated into the church.Wall paintings from the 15th century are known and traces remain in the south chancel aisle.
The well known Doom painting of the Last Judgement was commissioned between 1470 and 1500 from an unknown artist, who was probably an Englishman who had travelled in Europe and learned his skills in Flanders and other artistic centres. Doom paintings were not uncommon but few have survived and of those this is one of the largest, covering all the space above the chancel arch, most complete, and probably the best preserved. After the Reformation it was whitewashed over by 1593 and a panel displaying the arms of Elizabeth I set over it. In 1819 traces of colour were noticed under the whitewash which was carefully removed. The painting was recorded on paper and then covered by whitewash again! The whitewash was finally removed in 1881 and the painting restored in oils although the artist made some corrections. There is some dispute about the extent of these but most seems medieval such as the fact that there are are more bishops going to Hell than to Heaven and the figure of an ale-wife, who traditionally sold short measure, is being taken downwards.
During the 19th century there were many other alterations to the church and substantial repairs between 1902 and 1905. In the 18th century the churchyard was considered a disgrace and a scandal and the level had become so high with constant burials that in 1713 the churchwardens were ordered to lower the level by removing 6 inches (15 cm.) of soil every year. It was finally closed for burials in 1854. The parish registers from 1570 are held in the Wiltshire and Swindon History Centre in Chippenham.