Joseph Pease, a Darlington Quaker, obtained permission in the mid-1850s to mine coal near High Waterhouse, which was a farm on the Brancepeth estate.

The land was then owned by Gustavus Russell Hamilton-Russell and his wife Emma Maria, descendants of Sir Frederick Hamilton of Dromahere.

The company built housing for the new workers and a village grew up at the Mary Pit with residential areas south of the railway line.

When the village was first established, Anglican services were held in an old cottage near High Waterhouse Farm, which was also used as a school.

About 1866 Arthur Duncombe Shafto, rector of Brancepeth, proposed the building of a new church and school and the community began raising funds.

In February 1868 Lord Boyne of Brancepeth Castle donated one rood and 20 perches of land to the rector as a site for the new church.

Investment of this money was confirmed by Queen Victoria in 1878 to provide for a common fund for St. John's, Brandon and a proposed new district at Waterhouses.

It included a nave and chancel of cavity wall construction and was built of machine-pressed, sulphur-coloured bricks bearing a 'PEASE' stamp.

In 1892 an entry from the south porch was blocked to place an organ in the corner, and in 1897 a door was opened in the north vestry.