St. Thomas' Church dates back to the year 1836, when the need was felt for a second Anglican Church in St. John's to service the growing population in the east end of the city. An early painting of St. John's shows the original St. Thomas' as a little church with a prominent tower. This tower is still part of the present church. The church was used as a garrison church by the British soldiers stationed in St. John's until the late 1870s, which led to its nickname, "The Old Garrison Church".
The church escaped the ravages of the great fire which destroyed much of the town in 1846. A change in the wind direction caused the fire to veer off in another direction. The same year, a violent storm is said to have moved the whole building six inches. In an effort to stabilize the structure, the wings, which characterize the present building, were added five years later. In 1874, the increase in the number of parishioners led to the lengthening of the church by thirty feet. The church was again enlarged in 1883 by extending the chancel and adding a vestry and additional space for the organ. The last alteration to the building was made in 1903, when the chancel was again lengthened to provide seating accommodation for over 1300 people. A second great fire in 1892 led to the destruction of the Cathedral but again St. Thomas' was miraculously saved, though most of the city was destroyed.
In the late 1800s, Canon Wood Church Hall was built next to the church to provide an area for meetings and gatherings. Later, a school was built between the Hall and the Church (1927). In 1966 the Church Hall was destroyed in a fire and in 1974 when the St. Thomas' School was closed the building became the "new" Canon Wood Hall.
In 1922, in an area beneath the church, a space was dug out by hand for a small chapel for the Brotherhood of St. Andrew's, a men's service group. This chapel was restored and re-dedicated in 1982.