Most rural parishes are named for the village where the church is located, but there is no village of Heatherycleugh. Rather the church is located in the centre of Cowshill, while heatherycleugh is a gorge and burn that pass under the highway 3/4 mile to the west.
The original church was located about half a mile to the west of the present building. Early in the 20th century an encroaching quarry (ironically owned by the son of the vicar) forced the church to be demolished and moved stone by stone to be rebuilt in Cowshill in 1912. The text below is taken from "History, Topography and Directory of Durham, W. Whellan , 1856".
St Thomas' organ was installed by Nelson & Co. in 1915 and has been Grade II listed on the National Pipe Organ Register since 2010.