The church is named after St Ouen (or Audoen) of Rouen (Normandy), a saint who lived in the seventh century and was dedicated to him by the Anglo-Normans, who arrived in Dublin after 1172.
It was erected in 1190, possibly on the site of an older church dedicated to St. Columcille, dating to the seventh century.
Shortly afterwards the nave was lengthened (but also made narrower) and a century later a chancel was added.

In 1430 Henry VI, Lord of Ireland, authorised the erection of a chantry here, to be dedicated to St Anne.
 Its founders and successors were to be called the Guild or Fraternity of St Anne, usually called Saint Anne's Guild.
Six separate altars were set up in this chapel and were in constant use, financed by the wealthier parishioners.
In 1485 Sir Roland Fitz-Eustace, Earl Portlester, erected a new chapel next to the nave, in gratitude for his preservation from shipwreck near the site.

The turbulent events of the 16th century had its effects on the upkeep of the church and in 1630 the church was declared to be in a decrepit state.
The Archbishop, Lancelot Bulkeley, complained that "there is a guild there called St Anne's Guild that hath swallowed upp all the church meanes" (although chantries and guilds were suppressed during the Reformation in England and their property taken over by the king, in Ireland they survived, with varying vicissitudes, for many years).

 
Strenuous efforts were made over the next few years to repair the roof, steeple and pillars of the building, and the guild was ordered to contribute its share.
Funds were low – there were only sixteen Protestant houses in the parish.
 In 1671 Michael Boyle, the Church of Ireland Primate, ordered the "annoyance of the buttermilke market" under St Audoen's to be closed.
In 1673 an order was made to remove the tombs and tombstones from the church "to preserve the living from being injured by the dead".
St Anne's Guild, which had managed to secret away its extensive properties after the Reformation, and which had remained under Roman Catholic control, never did give up its holdings, despite several investigations and court orders lasting until 1702.

Although many repairs were carried out to the church and tower over the centuries, finance for the maintenance of the structures was always a problem, particularly in the 18th and 19th centuries.
By 1825, the church building itself was in a ruinous state (as reported by G. N. Wright) and "very few Protestants" remained in the parish.
As the finance to carry out substantial repairs was not available, parts of the church were closed off or unroofed.
As a consequence many ancient tombs gradually crumbled and memorials were removed or rendered illegible by exposure to the weather.
The church is named after St Ouen (or Audoen) of Rouen (Normandy), a saint who lived in the seventh century and was dedicated to him by the Anglo-Normans, who arrived in Dublin after 1172. It was erected in 1190, possibly on the site of an older church dedicated to St. Columcille, dating to the seventh century. Shortly afterwards the nave was lengthened (but also made narrower) and a century later a chancel was added.
In 1430 Henry VI, Lord of Ireland, authorised the erection of a chantry here, to be dedicated to St Anne.  Its founders and successors were to be called the Guild or Fraternity of St Anne, usually called Saint Anne's Guild. Six separate altars were set up in this chapel and were in constant use, financed by the wealthier parishioners. In 1485 Sir Roland Fitz-Eustace, Earl Portlester, erected a new chapel next to the nave, in gratitude for his preservation from shipwreck near the site.
The turbulent events of the 16th century had its effects on the upkeep of the church and in 1630 the church was declared to be in a decrepit state. The Archbishop, Lancelot Bulkeley, complained that "there is a guild there called St Anne's Guild that hath swallowed upp all the church meanes" (although chantries and guilds were suppressed during the Reformation in England and their property taken over by the king, in Ireland they survived, with varying vicissitudes, for many years).
 
Strenuous efforts were made over the next few years to repair the roof, steeple and pillars of the building, and the guild was ordered to contribute its share. Funds were low – there were only sixteen Protestant houses in the parish.  In 1671 Michael Boyle, the Church of Ireland Primate, ordered the "annoyance of the buttermilke market" under St Audoen's to be closed. In 1673 an order was made to remove the tombs and tombstones from the church "to preserve the living from being injured by the dead". St Anne's Guild, which had managed to secret away its extensive properties after the Reformation, and which had remained under Roman Catholic control, never did give up its holdings, despite several investigations and court orders lasting until 1702.
Although many repairs were carried out to the church and tower over the centuries, finance for the maintenance of the structures was always a problem, particularly in the 18th and 19th centuries. By 1825, the church building itself was in a ruinous state (as reported by G. N. Wright) and "very few Protestants" remained in the parish. As the finance to carry out substantial repairs was not available, parts of the church were closed off or unroofed. As a consequence many ancient tombs gradually crumbled and memorials were removed or rendered illegible by exposure to the weather.
St. Audoen's Church, Dublin (Church of Ireland)