The street is named after the church of St. Thomas, founded in 1175 near St. Catherine's church. The founder was William FitzAldelm, deputy and kinsman of King Henry II.
The church was dedicated to Thomas Beckett (St. Thomas the Martyr), who had recently been murdered in his cathedral at Canterbury by followers of the king. The church became a rich and powerful monastery, which controlled the Liberty of Thomas Court and Donore. In 1539 it was dissolved with all the monasteries by Henry VIII. Over the following 150 years the churches in the neighbourhood passed over to the reformed church, while Roman Catholic priests led a precarious existence tending to the larger part of the population, which remained faithful to the old religion.
From the mid-16th century the Lord of this Liberty was the Earl of Meath, whose family acquired the lands of the monastery from Henry VIII when he dissolved the monasteries.
In 1803 this street was the scene of the events surrounding the insurrection organised by Robert Emmet, where Lord Kilwarden was killed. Many of the participants in what turned out to be a riot were from this street and neighbouring streets.