It is believed that Holy Trinity is one of the 'Waterloo Churches'.
In 1818 the government of the day designated £1,000,000 for the purpose of building churches in populated areas as a ‘thank offering for peace’ after the victory over Napoleon at Waterloo in 1815, though additional funds were needed if a church was to be built. The architecture of the Church suggests that some of the funds for building Holy Trinity Church came from this 'thank-offering’.
In the summer of 1831 a ship carrying cholera docked in Sunderland. The outbreak soon began to spread throughout the north of England. As the death toll rose, the people of Stockton held meetings on how to protect their district. Though precautions were taken, cholera struck the town just four months later. Out of a population of 7,800 some 604 people contracted the disease and 124 deaths were recorded within the space of a few weeks.
The dead were originally going to be buried in the graveyard of the Parish Church but it was thought to be too close to the residential area of the High Street. The situation was saved by the last of the Prince Bishops of Durham, Bishop van Mildert, who granted a plot of land on the edge of town called Castle Park to the people of Stockton . Permission was given for the plot to be consecrated and there the bodies were buried in a communal grave called "The Monument".
Two years later, the Bishop gave a further five acres of land for a cemetery, church and parsonage to be built on this plot. Holy Trinity Church was erected on a site where farm buildings had stood since the Restoration.
The building of Holy Trinity, designed by John and Benjamin Green, began in 1834. It was consecrated on December 22, 1835. The church spire measured 200 feet high making it the tallest building in the area at the time. The top of the spire was lost during a gale in 1882.
Holy Trinity continued to serve the Anglican community of Stockton faithfully for many years but in September 1955 it was reported that the churchyard was to be converted into an open space.
The gravestones had become dilapidated and had to be removed. A number of these were in memory of master mariners who had sailed from the port of Stockton, one epitaph began, ‘Death to me little warning gave, and quickly called me to my grave.’ The stones and memorials were removed and were placed around the south wall of the churchyard.
In 1985 the building was taken over by the Greek Orthodox Church but was destroyed by fire in 1991 The cause of the fire was never established. The ruined church is now the site of many of Stockton's cultural events such as Stockton International Riverside Festival.